flake8 fixes

Author: Tieqiong

devutils/makesdist

@@ -10,12 +10,11 @@ import os
 import subprocess
 import sys
 import tarfile
+from setup import FALLBACK_VERSION, versiondata
 
 BASEDIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 sys.path.insert(0, BASEDIR)
 
-from setup import FALLBACK_VERSION, versiondata
-
 timestamp = versiondata.getint("DEFAULT", "timestamp")
 
 vfb = versiondata.get("DEFAULT", "version").split(".post")[0] + ".post0"

src/diffpy/structure/__init__.py

@@ -32,14 +32,13 @@
 from diffpy.structure.pdffitstructure import PDFFitStructure
 from diffpy.structure.structure import Structure
 from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
-
-# obtain version information
-
-"""Crystal structure container and parsers for structure formats."""
+from diffpy.structure.parsers import getParser
 
 # package version
 from diffpy.structure.version import __version__
 
+"""Crystal structure container and parsers for structure formats."""
+
 # top level routines
 
 
@@ -68,7 +67,6 @@ def loadStructure(filename, fmt="auto", **kw):
         Return a more specific PDFFitStructure type for 'pdffit'
         and 'discus' formats.
     """
-    from diffpy.structure.parsers import getParser
 
     p = getParser(fmt, **kw)
     rv = p.parseFile(filename)

src/diffpy/structure/mmlibspacegroups.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
-## Copyright 2002 by PyMMLib Development Group, http://pymmlib.sourceforge.net/
-## This code is part of the PyMMLib distribution and governed by
-## its license.  Please see the LICENSE_pymmlib file that should have been
-## included as part of this package.
+# Copyright 2002 by PyMMLib Development Group, http://pymmlib.sourceforge.net/
+# This code is part of the PyMMLib distribution and governed by
+# its license.  Please see the LICENSE_pymmlib file that should have been
+# included as part of this package.
 """Space groups defined as a part of the pymmlib.
 """
 
@@ -107,7 +107,7 @@
     Tr_34_34_34,
 )
 
-## spacegroup definitions
+# spacegroup definitions
 sg1 = SpaceGroup(
     number=1,
     num_sym_equiv=1,
@@ -7884,7 +7884,7 @@
 )
 
 
-## list of the space groups
+# list of the space groups
 mmLibSpaceGroupList = [
     sg1,
     sg2,

src/diffpy/structure/parsers/p_cif.py

@@ -460,7 +460,7 @@ def _parse_atom_site_aniso_label(self, block):
                 break
             idx = self.labelindex[lb]
             a = self.stru[idx]
-            if not lb in self.anisotropy:
+            if lb not in self.anisotropy:
                 a.anisotropy = True
                 self.anisotropy[lb] = True
             for fset, val in zip(prop_setters, values):
@@ -544,7 +544,7 @@ def _expandAsymmetricUnit(self, block):
         # setup anisotropy according to symmetry requirements
         # unless it was already explicitly set
         for ca, uisotropy in zip(self.stru, self.eau.Uisotropy):
-            if not ca.label in self.anisotropy:
+            if ca.label not in self.anisotropy:
                 ca.anisotropy = not uisotropy
                 self.anisotropy[ca.label] = ca.anisotropy
         # build a nested list of new atoms:

src/diffpy/structure/parsers/p_pdffit.py

@@ -54,17 +54,17 @@ def parseLines(self, lines):
                 stop -= 1
             ilines = iter(lines[:stop])
             # read header of PDFFit file
-            for l in ilines:
+            for line in ilines:
                 p_nl += 1
-                words = l.split()
+                words = line.split()
                 if len(words) == 0 or words[0][0] == "#":
                     continue
                 elif words[0] == "title":
-                    stru.title = l.lstrip()[5:].strip()
+                    stru.title = line.lstrip()[5:].strip()
                 elif words[0] == "scale":
                     stru.pdffit["scale"] = float(words[1])
                 elif words[0] == "sharp":
-                    l1 = l.replace(",", " ")
+                    l1 = line.replace(",", " ")
                     sharp_pars = [float(w) for w in l1.split()[1:]]
                     if len(sharp_pars) < 4:
                         stru.pdffit["delta2"] = sharp_pars[0]
@@ -77,21 +77,21 @@ def parseLines(self, lines):
                         stru.pdffit["rcut"] = sharp_pars[3]
                 elif words[0] == "spcgr":
                     key = "spcgr"
-                    start = l.find(key) + len(key)
-                    value = l[start:].strip()
+                    start = line.find(key) + len(key)
+                    value = line[start:].strip()
                     stru.pdffit["spcgr"] = value
                 elif words[0] == "shape":
-                    self._parse_shape(l)
+                    self._parse_shape(line)
                 elif words[0] == "cell":
                     cell_line_read = True
-                    l1 = l.replace(",", " ")
+                    l1 = line.replace(",", " ")
                     latpars = [float(w) for w in l1.split()[1:7]]
                     stru.lattice = Lattice(*latpars)
                 elif words[0] == "dcell":
-                    l1 = l.replace(",", " ")
+                    l1 = line.replace(",", " ")
                     stru.pdffit["dcell"] = [float(w) for w in l1.split()[1:7]]
                 elif words[0] == "ncell":
-                    l1 = l.replace(",", " ")
+                    l1 = line.replace(",", " ")
                     stru.pdffit["ncell"] = [int(w) for w in l1.split()[1:5]]
                 elif words[0] == "format":
                     if words[1] != "pdffit":
@@ -100,17 +100,17 @@ def parseLines(self, lines):
                 elif words[0] == "atoms" and cell_line_read:
                     break
                 else:
-                    self.ignored_lines.append(l)
+                    self.ignored_lines.append(line)
             # Header reading finished, check if required lines were present.
             if not cell_line_read:
                 emsg = "%d: file is not in PDFfit format" % p_nl
                 raise StructureFormatError(emsg)
             # Load data from atom entries.
             p_natoms = reduce(lambda x, y: x * y, stru.pdffit["ncell"])
             # we are now inside data block
-            for l in ilines:
+            for line in ilines:
                 p_nl += 1
-                wl1 = l.split()
+                wl1 = line.split()
                 element = wl1[0][0].upper() + wl1[0][1:].lower()
                 xyz = [float(w) for w in wl1[1:4]]
                 occ = float(wl1[4])
@@ -176,8 +176,8 @@ def toLines(self, stru):
         d_sigo = 0.0
         d_sigU = numpy.zeros((3, 3), dtype=float)
         # here we can start
-        l = "title  " + stru.title
-        lines.append(l.strip())
+        line = "title  " + stru.title
+        lines.append(line.strip())
         lines.append("format pdffit")
         lines.append("scale  %9.6f" % stru_pdffit["scale"])
         lines.append(

src/diffpy/structure/parsers/p_rawxyz.py

@@ -40,7 +40,7 @@ def parseLines(self, lines):
 
         Return Structure object or raise StructureFormatError.
         """
-        linefields = [l.split() for l in lines]
+        linefields = [line.split() for line in lines]
         # prepare output structure
         stru = Structure()
         # find first valid record

src/diffpy/structure/parsers/p_xcfg.py

@@ -215,12 +215,12 @@ def parseLines(self, lines):
                 else:
                     break
             # check header for consistency
-            if numpy.any(xcfg_H0_set == False):
+            if not numpy.all(xcfg_H0_set):
                 emsg = "H0 tensor is not properly defined"
                 raise StructureFormatError(emsg)
             p_auxnum = len(p_auxiliary) and max(p_auxiliary.keys()) + 1
             for i in range(p_auxnum):
-                if not i in p_auxiliary:
+                if i not in p_auxiliary:
                     p_auxiliary[i] = "aux%d" % i
             sorted_aux_keys = sorted(p_auxiliary.keys())
             if p_auxnum != 0:

src/diffpy/structure/parsers/p_xyz.py

@@ -40,7 +40,7 @@ def parseLines(self, lines):
 
         Return Structure object or raise StructureFormatError.
         """
-        linefields = [l.split() for l in lines]
+        linefields = [line.split() for line in lines]
         # prepare output structure
         stru = Structure()
         # find first valid record

src/diffpy/structure/spacegroupmod.py

@@ -1,14 +1,14 @@
 #!/usr/bin/env python
-## Copyright 2002 by PyMMLib Development Group, http://pymmlib.sourceforge.net/
-## This code is part of the PyMMLib distribution and governed by
-## its license.  Please see the LICENSE_pymmlib file that should have been
-## included as part of this package.
+# Copyright 2002 by PyMMLib Development Group, http://pymmlib.sourceforge.net/
+# This code is part of the PyMMLib distribution and governed by
+# its license.  Please see the LICENSE_pymmlib file that should have been
+# included as part of this package.
 """Symmetry operations as functions on vectors or arrays.
 """
 
 import numpy
 
-## 64 unique rotation matricies
+# 64 unique rotation matricies
 Rot_Z_mY_X = numpy.array([[0.0, 0.0, 1.0], [0.0, -1.0, 0.0], [1.0, 0.0, 0.0]], float)
 Rot_Y_mX_mZ = numpy.array([[0.0, 1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
 Rot_XmY_X_mZ = numpy.array([[1.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
@@ -74,7 +74,7 @@
 Rot_mZ_X_mY = numpy.array([[0.0, 0.0, -1.0], [1.0, 0.0, 0.0], [0.0, -1.0, 0.0]], float)
 Rot_Y_X_Z = numpy.array([[0.0, 1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
 
-## 32 unique translation vectors
+# 32 unique translation vectors
 Tr_0_0_34 = numpy.array([0.0, 0.0, 3.0 / 4.0], float)
 Tr_12_0_34 = numpy.array([1.0 / 2.0, 0.0, 3.0 / 4.0], float)
 Tr_0_0_56 = numpy.array([0.0, 0.0, 5.0 / 6.0], float)