skpkg: final step, merge branch cookie into main

doc/source/examples/distanceprinter.py

@@ -1,22 +1,25 @@
 #!/usr/bin/env python
 
-"""Demonstration of using PairQuantity class for a printout of pair distances
-in periodic and non-periodic structures."""
+"""Demonstration of using PairQuantity class for a printout of pair
+distances in periodic and non-periodic structures."""
 
 from diffpy.srreal.pairquantity import PairQuantity
 from diffpy.structure import Structure
 
 
 class DistancePrinter(PairQuantity):
-    """This PairQuantity class simply prints the visited pair distances and the
-    indices of the contributing atoms."""
+    """This PairQuantity class simply prints the visited pair distances
+    and the indices of the contributing atoms."""
 
     def _resetValue(self):
         self.count = 0
 
     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/lennardjones/ljcalculator.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-"""Demonstration of using PairQuantity class for calculation of Lennard Jones
-potential.
+"""Demonstration of using PairQuantity class for calculation of Lennard
+Jones potential.
 
 Vij = 4 * ( rij ** -12  -  rij ** -6 )
 """

doc/source/examples/parallelPDF.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
-"""Demonstration of parallel PDF calculation using the multiprocessing package.
+"""Demonstration of parallel PDF calculation using the multiprocessing
+package.
 
 A PDF of menthol structure is first calculated on a single core and then
 on all computer CPUs.  The script then compares both results and prints
@@ -25,7 +26,11 @@
 
 # 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 = '''
 /(
@@ -78,3 +78,8 @@ exclude = '''
   | tests/data
 )/
 '''
+
+[tool.docformatter]
+recursive = true
+wrap-summaries = 72
+wrap-descriptions = 72

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/_docstrings.py

@@ -18,7 +18,8 @@
 
 
 def get_registry_docstrings(cls):
-    """Build a dictionary of docstrings per each HasClassRegistry method.
+    """Build a dictionary of docstrings per each HasClassRegistry
+    method.
 
     Parameters
     ----------

src/diffpy/srreal/_final_imports.py

@@ -25,7 +25,8 @@
 
 
 def import_now():
-    """Import all Python modules that tweak extension-defined classes."""
+    """Import all Python modules that tweak extension-defined
+    classes."""
     global _import_now_called
     if _import_now_called:
         return

src/diffpy/srreal/atomradiitable.py

@@ -63,9 +63,9 @@ def clone(self):
         return copy.copy(self)
 
     def type(self):
-        """Unique string identifier of the CovalentRadiiTable type. This is
-        used for class registration and as an argument for the createByType
-        function.
+        """Unique string identifier of the CovalentRadiiTable type. This
+        is used for class registration and as an argument for the
+        createByType function.
 
         Return string.
         """

src/diffpy/srreal/attributes.py

@@ -36,7 +36,8 @@ def _getattr(self, name):
 
 
 def _setattr(self, name, value):
-    """Assign to C++ double attribute if Python attribute does not exist."""
+    """Assign to C++ double attribute if Python attribute does not
+    exist."""
     try:
         object.__getattribute__(self, name)
     except AttributeError:

src/diffpy/srreal/bondcalculator.py

@@ -43,8 +43,8 @@
 
 
 def _init_kwargs(self, **kwargs):
-    """Create a new instance of BondCalculator. Keyword arguments can be used
-    to configure calculator properties, for example:
+    """Create a new instance of BondCalculator. Keyword arguments can be
+    used to configure calculator properties, for example:
 
     bdc = BondCalculator(rmin=1.5, rmax=2.5)
 

src/diffpy/srreal/devutils/tunePeakPrecision.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
-"""Tune the peak precision parameter so that PDFCalculator gives equivalent
-results to diffpy.pdffit2.
+"""Tune the peak precision parameter so that PDFCalculator gives
+equivalent results to diffpy.pdffit2.
 
 Usage: tunePeakPrecision.py [qmax] [peakprecision] [createplot]
 """
@@ -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/eventticker.py

@@ -12,7 +12,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""Class EventTicker -- storage of modification times of dependent objects."""
+"""Class EventTicker -- storage of modification times of dependent
+objects."""
 
 
 # exported items

src/diffpy/srreal/overlapcalculator.py

@@ -12,7 +12,8 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-"""Class OverlapCalculator -- calculator of atom overlaps in a structure."""
+"""Class OverlapCalculator -- calculator of atom overlaps in a
+structure."""
 
 
 # exported items, these also makes them show in pydoc.
@@ -50,8 +51,8 @@
 
 
 def _init_kwargs(self, **kwargs):
-    """Create a new instance of OverlapCalculator. Keyword arguments can be
-    used to configure calculator properties, for example:
+    """Create a new instance of OverlapCalculator. Keyword arguments can
+    be used to configure calculator properties, for example:
 
     olc = OverlapCalculator(rmax=2.5)
 

src/diffpy/srreal/pairquantity.py

@@ -12,7 +12,8 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ##############################################################################
-"""Class PairQuantity    -- base class for Python defined calculators."""
+"""Class PairQuantity    -- base class for Python defined
+calculators."""
 
 
 # exported items

src/diffpy/srreal/parallel.py

@@ -43,8 +43,8 @@ def createParallelCalculator(pqobj, ncpu, pmap):
     """
 
     class ParallelPairQuantity(Attributes):
-        """Class for running parallel calculations.  This is a proxy class to
-        the wrapper PairQuantity type with the same interface.
+        """Class for running parallel calculations.  This is a proxy
+        class to the wrapper PairQuantity type with the same interface.
 
         Instance data:
 
@@ -70,7 +70,8 @@ def __init__(self, pqobj, ncpu, pmap):
             return
 
         def eval(self, stru=None):
-            """Perform parallel calculation and return internal value array.
+            """Perform parallel calculation and return internal value
+            array.
 
             stru -- object that can be converted to StructureAdapter,
                     e.g., example diffpy Structure or pyobjcryst Crystal.
@@ -163,7 +164,9 @@ 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))
@@ -206,7 +209,8 @@ def _fdel(self):
 
 
 def _parallelData(kwd):
-    """Helper for calculating and fetching raw results from a worker node."""
+    """Helper for calculating and fetching raw results from a worker
+    node."""
     pqobj = kwd["pqobj"]
     pqobj._setupParallelRun(kwd["cpuindex"], kwd["ncpu"])
     pqobj.eval()

src/diffpy/srreal/pdfbaseline.py

@@ -48,8 +48,9 @@
 
 
 def makePDFBaseline(name, fnc, replace=False, **dbattrs):
-    """Helper function for registering Python function as a PDFBaseline. This
-    is required for using Python function as PDFCalculator.baseline.
+    """Helper function for registering Python function as a PDFBaseline.
+    This is required for using Python function as
+    PDFCalculator.baseline.
 
     name     -- unique string name for registering Python function in the
                 global registry of PDFBaseline types.  This will be the
@@ -85,7 +86,9 @@ 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/pdfcalculator.py

@@ -86,7 +86,8 @@
 
 
 def _defineCommonInterface(cls):
-    """This function defines shared properties of PDF calculator classes."""
+    """This function defines shared properties of PDF calculator
+    classes."""
 
     cls.scale = propertyFromExtDoubleAttr(
         "scale",
@@ -161,10 +162,10 @@ def _defineCommonInterface(cls):
     )
 
     def _call_kwargs(self, structure=None, **kwargs):
-        """Calculate PDF for the given structure as an (r, G) tuple. Keyword
-        arguments can be used to configure calculator attributes, these
-        override any properties that may be passed from the structure, such as
-        spdiameter.
+        """Calculate PDF for the given structure as an (r, G) tuple.
+        Keyword arguments can be used to configure calculator
+        attributes, these override any properties that may be passed
+        from the structure, such as spdiameter.
 
         structure    -- a structure object to be evaluated.  Reuse the last
                         structure when None.

src/diffpy/srreal/pdfenvelope.py

@@ -77,8 +77,9 @@
 
 
 def makePDFEnvelope(name, fnc, replace=False, **dbattrs):
-    """Helper function for registering Python function as a PDFEnvelope. This
-    is required for using Python function as PDFCalculator envelope.
+    """Helper function for registering Python function as a PDFEnvelope.
+    This is required for using Python function as PDFCalculator
+    envelope.
 
     name     -- unique string name for registering Python function in the
                 global registry of PDFEnvelope types.  This will be the
@@ -115,7 +116,9 @@ 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