skpkg: pre-commit auto fixes with line length of 79

doc/source/examples/distanceprinter.py

@@ -16,7 +16,10 @@ def _resetValue(self):
 
     def _addPairContribution(self, bnds, sumscale):
         self.count += bnds.multiplicity() * sumscale / 2.0
-        print("%i %g %i %i" % (self.count, bnds.distance(), bnds.site0(), bnds.site1()))
+        print(
+            "%i %g %i %i"
+            % (self.count, bnds.distance(), bnds.site0(), bnds.site1())
+        )
         return
 
 

doc/source/examples/parallelPDF.py

@@ -25,7 +25,11 @@
 
 # configure options parsing
 parser = optparse.OptionParser("%prog [options]\n" + __doc__)
-parser.add_option("--pyobjcryst", action="store_true", help="Use pyobjcryst to load the CIF file.")
+parser.add_option(
+    "--pyobjcryst",
+    action="store_true",
+    help="Use pyobjcryst to load the CIF file.",
+)
 parser.allow_interspersed_args = True
 opts, args = parser.parse_args(sys.argv[1:])
 

news/pc-blackv2.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Configure ``black`` to have a linelength requirement of 79 characters.
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -57,7 +57,7 @@ ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
 [tool.black]
-line-length = 115
+line-length = 79
 include = '\.pyi?$'
 exclude = '''
 /(

setup.py

@@ -37,7 +37,8 @@ def get_boost_config():
         conda_prefix = os.environ.get("CONDA_PREFIX")
         if not conda_prefix:
             raise EnvironmentError(
-                "Neither BOOST_PATH nor CONDA_PREFIX are set. " "Please install Boost or set BOOST_PATH."
+                "Neither BOOST_PATH nor CONDA_PREFIX are set. "
+                "Please install Boost or set BOOST_PATH."
             )
         if os.name == "nt":
             inc = Path(conda_prefix) / "Library" / "include"
@@ -52,7 +53,8 @@ def get_objcryst_libraries():
     conda_prefix = os.environ.get("CONDA_PREFIX")
     if not conda_prefix:
         raise EnvironmentError(
-            "CONDA_PREFIX is not set. Please install ObjCryst using conda and activate the environment."
+            "CONDA_PREFIX is not set. "
+            "Please install ObjCryst using conda and activate the environment."
         )
     if os.name == "nt":
         libdir = Path(conda_prefix) / "Library" / "lib"
@@ -64,7 +66,8 @@ def get_objcryst_libraries():
         stem = Path(fn).stem
         if "objcryst" not in stem.lower():
             continue
-        # strip a leading "lib" so that setuptools does -lObjCryst, not -llibObjCryst
+        # strip a leading "lib"
+        # so that setuptools does -lObjCryst, not -llibObjCryst
         if os.name != "nt" and stem.startswith("lib"):
             stem = stem[3:]
         libs.append(stem)
@@ -99,7 +102,11 @@ def get_objcryst_libraries():
 
 def create_extensions():
     "Initialize Extension objects for the setup function."
-    ext = Extension("diffpy.srreal.srreal_ext", glob.glob("src/extensions/*.cpp"), **ext_kws)
+    ext = Extension(
+        "diffpy.srreal.srreal_ext",
+        glob.glob("src/extensions/*.cpp"),
+        **ext_kws,
+    )
     return [ext]
 
 

src/diffpy/srreal/devutils/tunePeakPrecision.py

@@ -108,7 +108,9 @@ def comparePDFCalculators(qmax, peakprecision=None):
     rv = {}
     rv["qmax"] = qmax
     rv["peakprecision"] = (
-        peakprecision is None and PDFCalculator()._getDoubleAttr("peakprecision") or peakprecision
+        peakprecision is None
+        and PDFCalculator()._getDoubleAttr("peakprecision")
+        or peakprecision
     )
     ttic = time.clock()
     rg0 = Gpdffit2(qmax)
@@ -175,7 +177,10 @@ def main():
     processCommandLineArguments()
     cmpdata = comparePDFCalculators(qmax, peakprecision)
     print(
-        ("qmax = %(qmax)g  pkprec = %(peakprecision)g  " + "grmsd = %(grmsd)g  t0 = %(t0).3f  t1 = %(t1).3f")
+        (
+            "qmax = %(qmax)g  pkprec = %(peakprecision)g  "
+            + "grmsd = %(grmsd)g  t0 = %(t0).3f  t1 = %(t1).3f"
+        )
         % cmpdata
     )
     if createplot:

src/diffpy/srreal/parallel.py

@@ -163,7 +163,9 @@ def proxymethod(self, *args, **kwargs):
         return proxymethod
 
     for n, f in inspect.getmembers(pqtype, inspect.isroutine):
-        ignore = n not in proxy_forced and (n.startswith("_") or hasattr(ParallelPairQuantity, n))
+        ignore = n not in proxy_forced and (
+            n.startswith("_") or hasattr(ParallelPairQuantity, n)
+        )
         if ignore:
             continue
         setattr(ParallelPairQuantity, n, _make_proxymethod(n, f))

src/diffpy/srreal/pdfbaseline.py

@@ -85,7 +85,9 @@ def fshiftedline(x, aline, bline):
     """
     from diffpy.srreal.wraputils import _wrapAsRegisteredUnaryFunction
 
-    rv = _wrapAsRegisteredUnaryFunction(PDFBaseline, name, fnc, replace=replace, **dbattrs)
+    rv = _wrapAsRegisteredUnaryFunction(
+        PDFBaseline, name, fnc, replace=replace, **dbattrs
+    )
     return rv
 
 

src/diffpy/srreal/pdfenvelope.py

@@ -115,7 +115,9 @@ def fexpdecay(x, expscale, exptail):
     """
     from diffpy.srreal.wraputils import _wrapAsRegisteredUnaryFunction
 
-    rv = _wrapAsRegisteredUnaryFunction(PDFEnvelope, name, fnc, replace=replace, **dbattrs)
+    rv = _wrapAsRegisteredUnaryFunction(
+        PDFEnvelope, name, fnc, replace=replace, **dbattrs
+    )
     return rv
 
 

src/diffpy/srreal/peakwidthmodel.py

@@ -20,7 +20,12 @@
 
 
 # exported items
-__all__ = ["PeakWidthModel", "ConstantPeakWidth", "DebyeWallerPeakWidth", "JeongPeakWidth"]
+__all__ = [
+    "PeakWidthModel",
+    "ConstantPeakWidth",
+    "DebyeWallerPeakWidth",
+    "JeongPeakWidth",
+]
 
 from diffpy.srreal import _final_imports
 from diffpy.srreal.srreal_ext import (

src/diffpy/srreal/scatteringfactortable.py

@@ -17,7 +17,14 @@
 
 
 # exported items, these also makes them show in pydoc.
-__all__ = ["ScatteringFactorTable", "SFTXray", "SFTElectron", "SFTNeutron", "SFTElectronNumber", "SFAverage"]
+__all__ = [
+    "ScatteringFactorTable",
+    "SFTXray",
+    "SFTElectron",
+    "SFTNeutron",
+    "SFTElectronNumber",
+    "SFAverage",
+]
 
 from diffpy.srreal.sfaverage import SFAverage
 from diffpy.srreal.srreal_ext import (

src/diffpy/srreal/sfaverage.py

@@ -150,7 +150,11 @@ def fromComposition(cls, composition, sftb, q=0):
         sfa.f1sum = 0.0 * q
         sfa.f2sum = 0.0 * q
         # resolve the lookup table object `tb`
-        tb = sftb if not isinstance(sftb, str) else ScatteringFactorTable.createByType(sftb)
+        tb = (
+            sftb
+            if not isinstance(sftb, str)
+            else ScatteringFactorTable.createByType(sftb)
+        )
         for smbl, cnt in sfa.composition.items():
             sfq = tb.lookup(smbl, q)
             sfa.f1sum += cnt * sfq

src/diffpy/srreal/structureconverters.py

@@ -26,8 +26,12 @@
 # Converters for Molecule and Crystal from pyobjcryst ------------------------
 
 
-RegisterStructureAdapter("pyobjcryst._pyobjcryst.Molecule", convertObjCrystMolecule)
-RegisterStructureAdapter("pyobjcryst._pyobjcryst.Crystal", convertObjCrystCrystal)
+RegisterStructureAdapter(
+    "pyobjcryst._pyobjcryst.Molecule", convertObjCrystMolecule
+)
+RegisterStructureAdapter(
+    "pyobjcryst._pyobjcryst.Crystal", convertObjCrystCrystal
+)
 
 # Converter for Structure class from diffpy.structure ------------------------
 
@@ -115,11 +119,15 @@ def _fetchMetadata(self, stru):
 # end of class _DiffPyStructureMetadata
 
 
-class DiffPyStructureAtomicAdapter(_DiffPyStructureMetadata, AtomicStructureAdapter):
+class DiffPyStructureAtomicAdapter(
+    _DiffPyStructureMetadata, AtomicStructureAdapter
+):
     pass
 
 
-class DiffPyStructurePeriodicAdapter(_DiffPyStructureMetadata, PeriodicStructureAdapter):
+class DiffPyStructurePeriodicAdapter(
+    _DiffPyStructureMetadata, PeriodicStructureAdapter
+):
     pass
 
 

src/diffpy/srreal/wraputils.py

@@ -59,7 +59,9 @@ def setattrFromKeywordArguments(obj, **kwargs):
     return
 
 
-def _wrapAsRegisteredUnaryFunction(cls, regname, fnc, replace=False, **dbattrs):
+def _wrapAsRegisteredUnaryFunction(
+    cls, regname, fnc, replace=False, **dbattrs
+):
     """Helper function for wrapping Python function as PDFBaseline or
     PDFEnvelope functor.  Not intended for direct usage, this function is
     rather called from makePDFBaseline or makePDFEnvelope wrappers.
@@ -149,7 +151,9 @@ def _pickle_getstate(self):
 
 def _pickle_setstate(self, state):
     if len(state) != 1:
-        emsg = "expected 1-item tuple in call to __setstate__, got " + repr(state)
+        emsg = "expected 1-item tuple in call to __setstate__, got " + repr(
+            state
+        )
         raise ValueError(emsg)
     self.__dict__.update(state[0])
     return

tests/conftest.py

@@ -70,6 +70,8 @@ def has_periodictable():
         del periodictable
     except ImportError:
         has_periodictable = False
-        logging.warning("Cannot import periodictable, periodictable tests skipped.")
+        logging.warning(
+            "Cannot import periodictable, periodictable tests skipped."
+        )
 
     return has_periodictable

tests/test_bondcalculator.py

@@ -134,7 +134,10 @@ def test_sites(self):
         self.assertEqual(5, numpy.max(bdc.sites0))
         self.assertEqual(0, numpy.min(bdc.sites1))
         self.assertEqual(5, numpy.max(bdc.sites1))
-        dij = [(tuple(d) + (i0, i1)) for d, i0, i1 in zip(bdc.directions, bdc.sites0, bdc.sites1)]
+        dij = [
+            (tuple(d) + (i0, i1))
+            for d, i0, i1 in zip(bdc.directions, bdc.sites0, bdc.sites1)
+        ]
         self.assertEqual(len(dij), len(set(dij)))
         bdc.maskAllPairs(False)
         bdc(self.rutile)
@@ -287,7 +290,10 @@ def test_sites(self):
         self.assertEqual(1, numpy.max(bdc.sites0))
         self.assertEqual(0, numpy.min(bdc.sites1))
         self.assertEqual(1, numpy.max(bdc.sites1))
-        dij = [(tuple(d) + (i0, i1)) for d, i0, i1 in zip(bdc.directions, bdc.sites0, bdc.sites1)]
+        dij = [
+            (tuple(d) + (i0, i1))
+            for d, i0, i1 in zip(bdc.directions, bdc.sites0, bdc.sites1)
+        ]
         self.assertEqual(len(dij), len(set(dij)))
         bdc.maskAllPairs(False)
         bdc(self.rutile)

tests/test_debyepdfcalculator.py

@@ -23,7 +23,9 @@ def setUp(self):
         if not TestDebyePDFCalculator.bucky:
             TestDebyePDFCalculator.bucky = loadDiffPyStructure("C60bucky.stru")
         if not TestDebyePDFCalculator.tio2rutile:
-            TestDebyePDFCalculator.tio2rutile = loadDiffPyStructure("TiO2_rutile-fit.stru")
+            TestDebyePDFCalculator.tio2rutile = loadDiffPyStructure(
+                "TiO2_rutile-fit.stru"
+            )
         return
 
     #   def tearDown(self):
@@ -166,7 +168,9 @@ def test_pickling(self):
         for a in dpdfc._namesOfDoubleAttributes():
             self.assertEqual(getattr(dpdfc, a), getattr(dpdfc1, a))
         self.assertEqual(13.3, dpdfc1.getEnvelope("sphericalshape").spdiameter)
-        self.assertEqual(dpdfc._namesOfDoubleAttributes(), dpdfc1._namesOfDoubleAttributes())
+        self.assertEqual(
+            dpdfc._namesOfDoubleAttributes(), dpdfc1._namesOfDoubleAttributes()
+        )
         self.assertEqual(dpdfc.usedenvelopetypes, dpdfc1.usedenvelopetypes)
         self.assertRaises(RuntimeError, pickle_with_attr, dpdfc, foo="bar")
         return

tests/test_overlapcalculator.py

@@ -91,7 +91,9 @@ def test_pickling(self):
             self.assertEqual(getattr(olc, a), getattr(olc1, a))
         self.assertFalse(olc1.getPairMask(1, 2))
         self.assertTrue(olc1.getPairMask(0, 0))
-        self.assertTrue(numpy.array_equal(olc.sitesquareoverlaps, olc1.sitesquareoverlaps))
+        self.assertTrue(
+            numpy.array_equal(olc.sitesquareoverlaps, olc1.sitesquareoverlaps)
+        )
         self.assertRaises(RuntimeError, pickle_with_attr, olc, foo="bar")
         return
 
@@ -140,13 +142,18 @@ def test_parallel(self):
         ncpu = 4
         self.pool = multiprocessing.Pool(processes=ncpu)
         olc = self.olc
-        polc = createParallelCalculator(OverlapCalculator(), ncpu, self.pool.imap_unordered)
+        polc = createParallelCalculator(
+            OverlapCalculator(), ncpu, self.pool.imap_unordered
+        )
         olc.atomradiitable.fromString("Ti:1.6, O:0.66")
         polc.atomradiitable = olc.atomradiitable
         self.assertTrue(numpy.array_equal(olc(self.rutile), polc(self.rutile)))
         self.assertTrue(olc.totalsquareoverlap > 0.0)
         self.assertEqual(olc.totalsquareoverlap, polc.totalsquareoverlap)
-        self.assertEqual(sorted(zip(olc.sites0, olc.sites1)), sorted(zip(polc.sites0, polc.sites1)))
+        self.assertEqual(
+            sorted(zip(olc.sites0, olc.sites1)),
+            sorted(zip(polc.sites0, polc.sites1)),
+        )
         olc.atomradiitable.resetAll()
         self.assertEqual(0.0, sum(olc(self.rutile)))
         self.assertEqual(0.0, sum(polc(self.rutile)))
@@ -288,7 +295,9 @@ def test_coordinations(self):
         self.assertFalse(numpy.any(olc.coordinations))
         olc.atomradiitable.fromString("Ti:1.6, O:0.66")
         olc(self.rutile)
-        self.assertTrue(numpy.array_equal([8, 8, 3, 3, 3, 3], olc.coordinations))
+        self.assertTrue(
+            numpy.array_equal([8, 8, 3, 3, 3, 3], olc.coordinations)
+        )
         return
 
     def test_coordinationByTypes(self):

tests/test_parallel.py

@@ -54,7 +54,9 @@ def test_parallel_evaluatortype(self):
         self.assertEqual("BASIC", ppdfc.evaluatortype)
         self.assertEqual("BASIC", pdfc.evaluatortype)
         ppdfc.evaluatortype = "BASIC"
-        self.assertRaises(ValueError, setattr, ppdfc, "evaluatortype", "OPTIMIZED")
+        self.assertRaises(
+            ValueError, setattr, ppdfc, "evaluatortype", "OPTIMIZED"
+        )
         return
 
     def test_parallel_pdf(self):
@@ -67,7 +69,9 @@ def test_parallel_pdf(self):
         r1, g1 = ppdfc1(self.cdse)
         self.assertTrue(numpy.array_equal(r0, r1))
         self.assertTrue(numpy.allclose(g0, g1))
-        ppdfc2 = createParallelCalculator(PDFCalculator(), self.ncpu, self.pool.imap_unordered)
+        ppdfc2 = createParallelCalculator(
+            PDFCalculator(), self.ncpu, self.pool.imap_unordered
+        )
         r2, g2 = ppdfc2(self.cdse)
         self.assertTrue(numpy.array_equal(r0, r2))
         self.assertTrue(numpy.allclose(g0, g2))
@@ -94,7 +98,9 @@ def test_parallel_bonds(self):
         pbc1 = createParallelCalculator(BondCalculator(), 3, map)
         d1 = pbc1(nickel)
         self.assertTrue(numpy.array_equal(d0, d1))
-        pbc2 = createParallelCalculator(BondCalculator(), self.ncpu, self.pool.imap_unordered)
+        pbc2 = createParallelCalculator(
+            BondCalculator(), self.ncpu, self.pool.imap_unordered
+        )
         d2 = pbc2(nickel)
         self.assertTrue(numpy.array_equal(d0, d2))
         bc.rmax = pbc1.rmax = pbc2.rmax = 2.5