Migration to pyproject

examples/distanceprinter.py

@@ -45,8 +45,8 @@ def _addPairContribution(self, bnds, sumscale):
 distprint._setDoubleAttr('rmax', 10)
 
 def get_pyobjcryst_sphalerite():
-    from pyobjcryst import loadCrystal
-    crst = loadCrystal('datafiles/sphalerite.cif')
+    from pyobjcryst.crystal import create_crystal_from_cif
+    crst = create_crystal_from_cif('datafiles/sphalerite.cif')
     return crst
 
 def main():

examples/parallelPDF.py

@@ -30,9 +30,9 @@
 # load menthol structure and make sure Uiso values are non-zero
 if opts.pyobjcryst:
     # use pyobjcryst if requested by the user
-    from pyobjcryst import loadCrystal
+    from pyobjcryst.crystal import create_crystal_crom_cif
     from numpy import pi
-    menthol = loadCrystal(mentholcif)
+    menthol = create_crystal_crom_cif(mentholcif)
     for sc in menthol.GetScatteringComponentList():
         sp = sc.mpScattPow
         sp.Biso = sp.Biso or 8 * pi**2 * Uisodefault

pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["setuptools>=62.0", "setuptools-git-versioning<2", "numpy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "diffpy.srreal"
+dynamic=['version']
+authors = [
+  { name="Simon J.L. Billinge group", email="[email protected]" },
+]
+maintainers = [
+  { name="Simon J.L. Billinge group", email="[email protected]" },
+]
+description = "calculators for PDF, bond valence sum, and other quantities based on atom pair interaction."
+keywords = ["PDF BVS atom overlap calculator real-space"]
+readme = "README.rst"
+requires-python = ">=3.9"
+dependencies = [
+	"diffpy.structure",
+]
+classifiers = [
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Education',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: BSD License',
+	'Operating System :: Microsoft :: Windows',
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: POSIX',
+        'Operating System :: Unix',
+        'Programming Language :: C++',
+        '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',
+        'Topic :: Software Development :: Libraries',
+]
+
+[project.urls]
+Homepage = "https://github.com/diffpy/diffpy.srreal/"
+Issues = "https://github.com/diffpy/diffpy.srreal/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 = ["diffpy*"]  # package names should match these glob patterns (["*"] by default)
+exclude = ["diffpy.srreal.tests*"]  # exclude packages matching these glob patterns (empty by default)
+namespaces = false  # to disable scanning PEP 420 namespaces (true by default)

setup.py

@@ -12,9 +12,9 @@
 import re
 import sys
 import glob
-from setuptools import setup, find_packages
+from setuptools import setup
 from setuptools import Extension
-from numpy.distutils.misc_util import get_numpy_include_dirs
+import numpy as np
 
 
 # Use this version when git data are not available, like in git zip archive.
@@ -27,7 +27,7 @@
         'libraries' : ['diffpy'],
         'extra_compile_args' : ['-std=c++11'],
         'extra_link_args' : [],
-        'include_dirs' : get_numpy_include_dirs(),
+        'include_dirs' : [np.get_include()],
 }
 
 # determine if we run with Python 3.
@@ -78,116 +78,12 @@ def create_extensions():
     return [ext]
 
 
-# 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, 'src/diffpy/srreal/version.cfg')
-gitarchivecfgfile = os.path.join(MYDIR, '.gitarchive.cfg')
-
-
-def gitinfo():
-    from subprocess import Popen, PIPE
-    kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
-    proc = Popen(['git', 'describe', '--match=v[[:digit:]]*'], **kw)
-    desc = proc.stdout.read()
-    proc = Popen(['git', 'log', '-1', '--format=%H %ct %ci'], **kw)
-    glog = proc.stdout.read()
-    rv = {}
-    rv['version'] = '.post'.join(desc.strip().split('-')[:2]).lstrip('v')
-    rv['commit'], rv['timestamp'], rv['date'] = glog.strip().split(None, 2)
-    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: v(\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()
-
-with open(os.path.join(MYDIR, 'README.rst')) as fp:
-    long_description = fp.read()
-
-# define distribution
+# Extensions not included in pyproject.toml
 setup_args = dict(
-    name = "diffpy.srreal",
-    version = versiondata.get('DEFAULT', 'version'),
-    packages = find_packages(os.path.join(MYDIR, 'src')),
-    package_dir = {'' : 'src'},
-    test_suite = 'diffpy.srreal.tests',
-    include_package_data = True,
     ext_modules = [],
-    install_requires = [
-        'diffpy.structure',
-    ],
-    zip_safe = False,
-
-    author = "Simon J.L. Billinge group",
-    author_email = "[email protected]",
-    maintainer = "Pavol Juhas",
-    maintainer_email = "[email protected]",
-    description = ("calculators for PDF, bond valence sum, and other "
-                   "quantities based on atom pair interaction."),
-    long_description = long_description,
-    long_description_content_type = 'text/x-rst',
-    license = 'BSD-style license',
-    url = "https://github.com/diffpy/diffpy.srreal/",
-    keywords = "PDF BVS atom overlap calculator real-space",
-    classifiers = [
-        # List of possible values at
-        # http://pypi.python.org/pypi?:action=list_classifiers
-        'Development Status :: 5 - Production/Stable',
-        'Environment :: Console',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Education',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: POSIX',
-        'Operating System :: Unix',
-        'Programming Language :: C++',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Topic :: Scientific/Engineering :: Chemistry',
-        'Topic :: Scientific/Engineering :: Physics',
-        'Topic :: Software Development :: Libraries',
-    ],
 )
 
+
 if __name__ == '__main__':
     setup_args['ext_modules'] = create_extensions()
     setup(**setup_args)

src/diffpy/srreal/_version_data.py

@@ -23,21 +23,22 @@
 
 import os.path
 
-from pkg_resources import resource_filename
+from importlib.resources import files, as_file
 
 
 # obtain version information from the version.cfg file
 cp = dict(version='', date='', commit='', timestamp='0')
-fcfg = resource_filename(__name__, 'version.cfg')
-if not os.path.isfile(fcfg):    # pragma: no cover
-    from warnings import warn
-    warn('Package metadata not found, execute "./setup.py egg_info".')
-    fcfg = os.devnull
-with open(fcfg) as fp:
-    kwords = [[w.strip() for w in line.split(' = ', 1)]
-              for line in fp if line[:1].isalpha() and ' = ' in line]
-assert all(w[0] in cp for w in kwords), "received unrecognized keyword"
-cp.update(kwords)
+ref = files(__package__) / 'version.cfg'
+with as_file(ref) as fcfg:
+    if not os.path.isfile(fcfg):    # pragma: no cover
+        from warnings import warn
+        warn('Package metadata not found, execute "./setup.py egg_info".')
+        fcfg = os.devnull
+    with open(fcfg) as fp:
+        kwords = [[w.strip() for w in line.split(' = ', 1)]
+                  for line in fp if line[:1].isalpha() and ' = ' in line]
+    assert all(w[0] in cp for w in kwords), "received unrecognized keyword"
+    cp.update(kwords)
 
 __version__ = cp['version']
 __date__ = cp['date']

src/diffpy/srreal/tests/__init__.py

@@ -43,30 +43,31 @@ def testsuite(pattern=''):
     import re
     from os.path import dirname
     from itertools import chain
-    from pkg_resources import resource_filename
+    from importlib.resources import files, as_file
     loader = unittest.defaultTestLoader
-    thisdir = resource_filename(__name__, '')
-    depth = __name__.count('.') + 1
-    topdir = thisdir
-    for i in range(depth):
-        topdir = dirname(topdir)
-    suite_all = loader.discover(thisdir, top_level_dir=topdir)
-    # always filter the suite by pattern to test-cover the selection code.
-    suite = unittest.TestSuite()
-    rx = re.compile(pattern)
-    tsuites = list(chain.from_iterable(suite_all))
-    tsok = all(isinstance(ts, unittest.TestSuite) for ts in tsuites)
-    if not tsok:    # pragma: no cover
-        return suite_all
-    tcases = chain.from_iterable(tsuites)
-    for tc in tcases:
-        tcwords = tc.id().split('.')
-        shortname = '.'.join(tcwords[-3:])
-        if rx.search(shortname):
-            suite.addTest(tc)
-    # verify all tests are found for an empty pattern.
-    assert pattern or suite_all.countTestCases() == suite.countTestCases()
-    return suite
+    ref = files(__package__)
+    with as_file(ref) as thisdir:
+        depth = __name__.count('.') + 1
+        topdir = thisdir
+        for i in range(depth):
+            topdir = dirname(topdir)
+        suite_all = loader.discover(thisdir, top_level_dir=topdir)
+        # always filter the suite by pattern to test-cover the selection code.
+        suite = unittest.TestSuite()
+        rx = re.compile(pattern)
+        tsuites = list(chain.from_iterable(suite_all))
+        tsok = all(isinstance(ts, unittest.TestSuite) for ts in tsuites)
+        if not tsok:    # pragma: no cover
+            return suite_all
+        tcases = chain.from_iterable(tsuites)
+        for tc in tcases:
+            tcwords = tc.id().split('.')
+            shortname = '.'.join(tcwords[-3:])
+            if rx.search(shortname):
+                suite.addTest(tc)
+        # verify all tests are found for an empty pattern.
+        assert pattern or suite_all.countTestCases() == suite.countTestCases()
+        return suite
 
 
 def test():

src/diffpy/srreal/tests/testoverlapcalculator.py

@@ -200,7 +200,7 @@ def test_gradients(self):
         tso0 = olc.totalsquareoverlap
         dx = 1e-8
         rutile2 = loadDiffPyStructure('rutile.cif')
-        rutile2[2].xyz_cartn += [dx, 0.0, 0.0]
+        rutile2[2].xyz_cartn[0] += dx
         olc.eval(rutile2)
         g2nx = (olc.totalsquareoverlap - tso0) / dx
         self.assertAlmostEqual(g2[0], g2nx, 6)

src/diffpy/srreal/tests/testutils.py

@@ -62,9 +62,9 @@ def datafile(filename):
 
 
 def loadObjCrystCrystal(filename):
-    from pyobjcryst import loadCrystal
+    from pyobjcryst.crystal import create_crystal_from_cif
     fullpath = datafile(filename)
-    crst = loadCrystal(fullpath)
+    crst = create_crystal_from_cif(fullpath)
     return crst