skpkg: apply black to all files in the project directory

Author: kwagoner94

devutils/sgtbx_extra_groups.py

@@ -16,7 +16,12 @@
 import numpy
 from cctbx import sgtbx
 
-from diffpy.structure.spacegroups import IsSpaceGroupIdentifier, SpaceGroup, SymOp, mmLibSpaceGroupList
+from diffpy.structure.spacegroups import (
+    IsSpaceGroupIdentifier,
+    SpaceGroup,
+    SymOp,
+    mmLibSpaceGroupList,
+)
 
 
 def tupleToSGArray(tpl):

doc/source/conf.py

@@ -221,7 +221,13 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "diffpy.structure.tex", "diffpy.structure Documentation", ab_authors, "manual"),
+    (
+        "index",
+        "diffpy.structure.tex",
+        "diffpy.structure Documentation",
+        ab_authors,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -249,7 +255,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "diffpy.structure", "diffpy.structure Documentation", ab_authors, 1)]
+man_pages = [
+    (
+        "index",
+        "diffpy.structure",
+        "diffpy.structure Documentation",
+        ab_authors,
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False

pyproject.toml

@@ -55,7 +55,7 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 dependencies = {file = ["requirements/pip.txt"]}
 
 [tool.black]
-line-length = 115
+line-length = 79
 include = '\.pyi?$'
 exclude = '''
 /(

src/diffpy/structure/__init__.py

@@ -42,7 +42,11 @@
 from diffpy.structure.parsers import getParser
 from diffpy.structure.pdffitstructure import PDFFitStructure
 from diffpy.structure.structure import Structure
-from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
+from diffpy.structure.structureerrors import (
+    LatticeError,
+    StructureFormatError,
+    SymmetryError,
+)
 
 # package version
 from diffpy.structure.version import __version__

src/diffpy/structure/_legacy_importer.py

@@ -80,7 +80,11 @@ def exec_module(self, module):
 # ----------------------------------------------------------------------------
 
 # show deprecation warning for diffpy.Structure
-warn(WMSG.format("diffpy.Structure", "diffpy.structure"), DeprecationWarning, stacklevel=2)
+warn(
+    WMSG.format("diffpy.Structure", "diffpy.structure"),
+    DeprecationWarning,
+    stacklevel=2,
+)
 
 # install meta path finder for diffpy.Structure submodules
 sys.meta_path.append(FindRenamedStructureModule())

src/diffpy/structure/apps/__init__.py

@@ -13,5 +13,4 @@
 #
 ##############################################################################
 
-"""Script applications that use the `diffpy.structure` package.
-"""
+"""Script applications that use the `diffpy.structure` package."""

src/diffpy/structure/apps/anyeye.py

@@ -71,7 +71,11 @@ def usage(style=None):
     myname = os.path.basename(sys.argv[0])
     msg = __doc__.replace("anyeye", myname)
     if style == "brief":
-        msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
+        msg = (
+            msg.split("\n")[1]
+            + "\n"
+            + "Try `%s --help' for more information." % myname
+        )
     else:
         from diffpy.structure.parsers import inputFormats
 
@@ -139,7 +143,10 @@ def convertStructureFile(pd):
     if pd["formula"]:
         formula = pd["formula"]
         if len(formula) != len(stru):
-            emsg = "Formula has %i atoms while structure %i" % (len(formula), len(stru))
+            emsg = "Formula has %i atoms while structure %i" % (
+                len(formula),
+                len(stru),
+            )
             raise RuntimeError(emsg)
         for a, el in zip(stru, formula):
             a.element = el
@@ -218,7 +225,9 @@ def main():
     pd["watch"] = False
     try:
         opts, args = getopt.getopt(
-            sys.argv[1:], "f:whV", ["formula=", "watch", "viewer=", "formats=", "help", "version"]
+            sys.argv[1:],
+            "f:whV",
+            ["formula=", "watch", "viewer=", "formats=", "help", "version"],
         )
     except getopt.GetoptError as errmsg:
         print(errmsg, file=sys.stderr)

src/diffpy/structure/apps/transtru.py

@@ -50,7 +50,11 @@ def usage(style=None):
     myname = os.path.basename(sys.argv[0])
     msg = __doc__.replace("transtru", myname)
     if style == "brief":
-        msg = msg.split("\n")[1] + "\n" + "Try `%s --help' for more information." % myname
+        msg = (
+            msg.split("\n")[1]
+            + "\n"
+            + "Try `%s --help' for more information." % myname
+        )
     else:
         from diffpy.structure.parsers import inputFormats, outputFormats
 
@@ -99,7 +103,10 @@ def main():
             print("'%s' is not valid output format" % outfmt, file=sys.stderr)
             sys.exit(2)
     except ValueError:
-        print("invalid format specification '%s' does not contain .." % args[0], file=sys.stderr)
+        print(
+            "invalid format specification '%s' does not contain .." % args[0],
+            file=sys.stderr,
+        )
         sys.exit(2)
     # ready to do some real work
     try:

src/diffpy/structure/atom.py

@@ -170,7 +170,9 @@ def msdLat(self, vl):
         lat = self.lattice or cartesian_lattice
         vln = numpy.array(vl, dtype=float) / lat.norm(vl)
         G = lat.metrics
-        rhs = numpy.array([G[0] * lat.ar, G[1] * lat.br, G[2] * lat.cr], dtype=float)
+        rhs = numpy.array(
+            [G[0] * lat.ar, G[1] * lat.br, G[2] * lat.cr], dtype=float
+        )
         rhs = numpy.dot(rhs, vln)
         msd = numpy.dot(rhs, numpy.dot(self.U, rhs))
         return msd
@@ -202,7 +204,13 @@ def msdCart(self, vc):
     def __repr__(self):
         """String representation of this Atom."""
         xyz = self.xyz
-        s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (self.element, xyz[0], xyz[1], xyz[2], self.occupancy)
+        s = "%-4s %8.6f %8.6f %8.6f %6.4f" % (
+            self.element,
+            xyz[0],
+            xyz[1],
+            xyz[2],
+            self.occupancy,
+        )
         return s
 
     def __copy__(self, target=None):
@@ -354,13 +362,19 @@ def _set_Uij(self, i, j, value):
         """
 
     U11 = property(
-        lambda self: self._get_Uij(0, 0), lambda self, value: self._set_Uij(0, 0, value), doc=_doc_uii.format(0)
+        lambda self: self._get_Uij(0, 0),
+        lambda self, value: self._set_Uij(0, 0, value),
+        doc=_doc_uii.format(0),
     )
     U22 = property(
-        lambda self: self._get_Uij(1, 1), lambda self, value: self._set_Uij(1, 1, value), doc=_doc_uii.format(1)
+        lambda self: self._get_Uij(1, 1),
+        lambda self, value: self._set_Uij(1, 1, value),
+        doc=_doc_uii.format(1),
     )
     U33 = property(
-        lambda self: self._get_Uij(2, 2), lambda self, value: self._set_Uij(2, 2, value), doc=_doc_uii.format(2)
+        lambda self: self._get_Uij(2, 2),
+        lambda self, value: self._set_Uij(2, 2, value),
+        doc=_doc_uii.format(2),
     )
 
     _doc_uij = """
@@ -371,13 +385,19 @@ def _set_Uij(self, i, j, value):
         """
 
     U12 = property(
-        lambda self: self._get_Uij(0, 1), lambda self, value: self._set_Uij(0, 1, value), doc=_doc_uij.format(0, 1)
+        lambda self: self._get_Uij(0, 1),
+        lambda self, value: self._set_Uij(0, 1, value),
+        doc=_doc_uij.format(0, 1),
     )
     U13 = property(
-        lambda self: self._get_Uij(0, 2), lambda self, value: self._set_Uij(0, 2, value), doc=_doc_uij.format(0, 2)
+        lambda self: self._get_Uij(0, 2),
+        lambda self, value: self._set_Uij(0, 2, value),
+        doc=_doc_uij.format(0, 2),
     )
     U23 = property(
-        lambda self: self._get_Uij(1, 2), lambda self, value: self._set_Uij(1, 2, value), doc=_doc_uij.format(1, 2)
+        lambda self: self._get_Uij(1, 2),
+        lambda self, value: self._set_Uij(1, 2, value),
+        doc=_doc_uij.format(1, 2),
     )
 
     # clean local variables

src/diffpy/structure/expansion/supercell_mod.py

@@ -13,8 +13,7 @@
 #
 ##############################################################################
 
-"""This module contains functions for simple `Structure` manipulation.
-"""
+"""This module contains functions for simple `Structure` manipulation."""
 
 import numpy
 
@@ -69,7 +68,12 @@ def supercell(S, mno):
         return newS
 
     # back to business
-    ijklist = [(i, j, k) for i in range(mno[0]) for j in range(mno[1]) for k in range(mno[2])]
+    ijklist = [
+        (i, j, k)
+        for i in range(mno[0])
+        for j in range(mno[1])
+        for k in range(mno[2])
+    ]
     # numpy.floor returns float array
     mnofloats = numpy.array(mno, dtype=float)
 
@@ -84,7 +88,9 @@ def supercell(S, mno):
     newS.__setitem__(slice(None), newAtoms, copy=False)
 
     # take care of lattice parameters
-    newS.lattice.setLatPar(a=mno[0] * S.lattice.a, b=mno[1] * S.lattice.b, c=mno[2] * S.lattice.c)
+    newS.lattice.setLatPar(
+        a=mno[0] * S.lattice.a, b=mno[1] * S.lattice.b, c=mno[2] * S.lattice.c
+    )
     return newS