[pre-commit.ci] auto fixes from pre-commit hooks

Author: pre-commit-ci[bot]

devutils/makesdist

@@ -1,51 +1,57 @@
 #!/usr/bin/env python
 
-'''Create source distribution tar.gz archive, where each file belongs
+"""Create source distribution tar.gz archive, where each file belongs
 to a root user and modification time is set to the git commit time.
-'''
+"""
 
-import sys
+import glob
+import gzip
 import os
 import subprocess
-import glob
+import sys
 import tarfile
-import gzip
 
 BASEDIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 sys.path.insert(0, BASEDIR)
 
-from setup import versiondata, FALLBACK_VERSION
-timestamp = versiondata.getint('DEFAULT', 'timestamp')
+from setup import FALLBACK_VERSION, versiondata
 
-vfb = versiondata.get('DEFAULT', 'version').split('.post')[0] + '.post0'
+timestamp = versiondata.getint("DEFAULT", "timestamp")
+
+vfb = versiondata.get("DEFAULT", "version").split(".post")[0] + ".post0"
 emsg = "Invalid FALLBACK_VERSION. Expected %r got %r."
 assert vfb == FALLBACK_VERSION, emsg % (vfb, FALLBACK_VERSION)
 
+
 def inform(s):
     sys.stdout.write(s)
     sys.stdout.flush()
     return
 
+
 inform('Run "setup.py sdist --formats=tar" ')
-cmd_sdist = [sys.executable] + 'setup.py sdist --formats=tar'.split()
-ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, 'w'))
-if ec:  sys.exit(ec)
+cmd_sdist = [sys.executable] + "setup.py sdist --formats=tar".split()
+ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, "w"))
+if ec:
+    sys.exit(ec)
 inform("[done]\n")
 
-tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
+tarname = max(glob.glob(BASEDIR + "/dist/*.tar"), key=os.path.getmtime)
 
 tfin = tarfile.open(tarname)
-fpout = gzip.GzipFile(tarname + '.gz', 'w', mtime=0)
-tfout = tarfile.open(fileobj=fpout, mode='w')
+fpout = gzip.GzipFile(tarname + ".gz", "w", mtime=0)
+tfout = tarfile.open(fileobj=fpout, mode="w")
+
 
 def fixtarinfo(tinfo):
     tinfo.uid = tinfo.gid = 0
-    tinfo.uname = tinfo.gname = 'root'
+    tinfo.uname = tinfo.gname = "root"
     tinfo.mtime = timestamp
     tinfo.mode &= ~0o022
     return tinfo
 
-inform('Filter %s --> %s.gz ' % (2 * (os.path.basename(tarname),)))
+
+inform("Filter %s --> %s.gz " % (2 * (os.path.basename(tarname),)))
 for ti in tfin:
     tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
 

devutils/sgtbx_extra_groups.py

@@ -1,28 +1,31 @@
 #!/usr/bin/env python
 
-'''Quick and extremely dirty script for generating code for SpaceGroup that
+"""Quick and extremely dirty script for generating code for SpaceGroup that
 are defined in cctbx, but not in mmLib.  It was used to generate module
 sgtbxspacegroups.
 
 This is a utility script that should not be included with code distribution.
 
 Not to be included with code distributions.
-'''
+"""
 
 
-import re
 import math
+import re
+
 import numpy
-from diffpy.structure.spacegroups import SpaceGroup, SymOp
-from diffpy.structure.spacegroups import mmLibSpaceGroupList
-from diffpy.structure.spacegroups import IsSpaceGroupIdentifier
 from cctbx import sgtbx
 
+from diffpy.structure.spacegroups import IsSpaceGroupIdentifier, SpaceGroup, SymOp, mmLibSpaceGroupList
+
+
 def tupleToSGArray(tpl):
     if not _rtarrays:
         import diffpy.structure.SpaceGroups as sgmod
+
         for n in dir(sgmod):
-            if not n.startswith('Rot_') and not n.startswith('Tr_'): continue
+            if not n.startswith("Rot_") and not n.startswith("Tr_"):
+                continue
             a = getattr(sgmod, n)
             t = tuple(a.flatten())
             _rtarrays[t] = a
@@ -31,29 +34,30 @@ def tupleToSGArray(tpl):
         if tpl not in _rtarrays:
             _rtarrays[tpl] = numpy.array(tpl, dtype=float)
     return _rtarrays[tpl]
+
+
 _rtarrays = {}
 
 
 def mmSpaceGroupFromSymbol(symbol):
-    """Construct SpaceGroup instance from a string symbol using sgtbx data.
-    """
+    """Construct SpaceGroup instance from a string symbol using sgtbx data."""
     sginfo = sgtbx.space_group_info(symbol)
     symop_list = []
     symop_list = getSymOpList(sginfo.group())
     sgtype = sginfo.type()
     uhm = sgtype.lookup_symbol()
     sgsmbls = sgtbx.space_group_symbols(uhm)
     kw = {}
-    kw['number'] = sgtype.number()
-    kw['num_sym_equiv'] = len(symop_list)
-    kw['num_primitive_sym_equiv'] = countUniqueRotations(symop_list)
-    kw['short_name'] = sgsmbls.hermann_mauguin().replace(' ', '')
+    kw["number"] = sgtype.number()
+    kw["num_sym_equiv"] = len(symop_list)
+    kw["num_primitive_sym_equiv"] = countUniqueRotations(symop_list)
+    kw["short_name"] = sgsmbls.hermann_mauguin().replace(" ", "")
     pgt = sgsmbls.point_group_type()
-    pgn = "PG" + re.sub(r'-(\d)', '\\1bar', pgt)
-    kw['point_group_name'] = pgn
-    kw['crystal_system'] = sgsmbls.crystal_system().upper()
-    kw['pdb_name'] = sgsmbls.hermann_mauguin()
-    kw['symop_list'] = symop_list
+    pgn = "PG" + re.sub(r"-(\d)", "\\1bar", pgt)
+    kw["point_group_name"] = pgn
+    kw["crystal_system"] = sgsmbls.crystal_system().upper()
+    kw["pdb_name"] = sgsmbls.hermann_mauguin()
+    kw["symop_list"] = symop_list
     mmsg = SpaceGroup(**kw)
     return mmsg
 
@@ -87,7 +91,8 @@ def countUniqueRotations(symop_list):
 
 
 def cmpSpaceGroups(sg0, sg1):
-    if sg0 is sg1:  return True
+    if sg0 is sg1:
+        return True
     s0 = hashMMSpaceGroup(sg0)
     s1 = hashMMSpaceGroup(sg1)
     return s0 == s1
@@ -100,6 +105,8 @@ def findEquivalentMMSpaceGroup(grp):
             _equivmmsg.setdefault(ssgn, sgn)
     ssg = hashSgtbxGroup(grp)
     return _equivmmsg.get(ssg)
+
+
 _equivmmsg = {}
 
 
@@ -112,24 +119,27 @@ def findEquivalentSgtbxSpaceGroup(sgmm):
             _equivsgtbx.setdefault(hgrp, grp)
     hgmm = hashMMSpaceGroup(sgmm)
     return _equivsgtbx.get(hgmm)
+
+
 _equivsgtbx = {}
 
 
 def hashMMSpaceGroup(sg):
     lines = [str(sg.number % 1000)] + sorted(map(str, sg.iter_symops()))
-    s = '\n'.join(lines)
+    s = "\n".join(lines)
     return s
 
 
 def hashSgtbxGroup(grp):
     n = grp.type().number()
     lines = [str(n)] + sorted(map(str, getSymOpList(grp)))
-    s = '\n'.join(lines)
+    s = "\n".join(lines)
     return s
 
+
 sgnumbers = [sg.number for sg in mmLibSpaceGroupList]
 
-_SGsrc = '''\
+_SGsrc = """\
 sg%(number)i = SpaceGroup(
     number = %(number)i,
     num_sym_equiv = %(num_sym_equiv)i,
@@ -142,32 +152,37 @@ def hashSgtbxGroup(grp):
         @SYMOPS@
     ]
 )
-'''
+"""
+
 
 def SGCode(mmsg):
     src0 = _SGsrc % mmsg.__dict__
-    src1 = src0.replace('@SYMOPS@', SymOpsCode(mmsg))
+    src1 = src0.replace("@SYMOPS@", SymOpsCode(mmsg))
     return src1
 
 
 def SymOpsCode(mmsg):
-    lst = ["%8s%s," % ('', SymOpCode(op)) for op in mmsg.iter_symops()]
-    src = '\n'.join(lst).strip()
+    lst = ["%8s%s," % ("", SymOpCode(op)) for op in mmsg.iter_symops()]
+    src = "\n".join(lst).strip()
     return src
 
 
 def SymOpCode(op):
     if not _rtnames:
         import diffpy.structure.SpaceGroups as sgmod
+
         for n in dir(sgmod):
-            if not n.startswith('Rot_') and not n.startswith('Tr_'): continue
+            if not n.startswith("Rot_") and not n.startswith("Tr_"):
+                continue
             a = getattr(sgmod, n)
             at = tuple(a.flatten())
-            _rtnames[at] = 'sgmod.' + n
+            _rtnames[at] = "sgmod." + n
     nR = _rtnames[tuple(op.R.flatten())]
     nt = _rtnames[tuple(op.t)]
-    src = 'SymOp(%s, %s)' % (nR, nt)
+    src = "SymOp(%s, %s)" % (nR, nt)
     return src
+
+
 _rtnames = {}
 
 
@@ -176,16 +191,20 @@ def main():
     for smbls in sgtbx.space_group_symbol_iterator():
         uhm = smbls.universal_hermann_mauguin()
         grp = sgtbx.space_group_info(uhm).group()
-        if findEquivalentMMSpaceGroup(grp): continue
-        shn = smbls.hermann_mauguin().replace(' ', '')
-        if IsSpaceGroupIdentifier(shn): continue
+        if findEquivalentMMSpaceGroup(grp):
+            continue
+        shn = smbls.hermann_mauguin().replace(" ", "")
+        if IsSpaceGroupIdentifier(shn):
+            continue
         sg = mmSpaceGroupFromSymbol(uhm)
         hsg = hashMMSpaceGroup(sg)
-        if hsg in duplicates: continue
+        if hsg in duplicates:
+            continue
         adjustMMSpaceGroupNumber(sg)
         duplicates.add(hsg)
         print(SGCode(sg))
     return
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     main()

doc/source/api/diffpy.structure.applications.rst

@@ -26,4 +26,3 @@ diffpy.structure.applications.anyeye module
     :members:
     :undoc-members:
     :show-inheritance:
-

doc/source/api/diffpy.structure.apps.rst

@@ -26,4 +26,3 @@ diffpy.structure.apps.anyeye module
     :members:
     :undoc-members:
     :show-inheritance:
-

doc/source/api/diffpy.structure.expansion.rst

@@ -34,4 +34,3 @@ diffpy.structure.expansion.supercell_mod module
     :members:
     :undoc-members:
     :show-inheritance:
-

doc/source/api/diffpy.structure.parsers.rst

@@ -90,4 +90,3 @@ diffpy.structure.parsers.p_xyz module
     :members:
     :undoc-members:
     :show-inheritance:
-

doc/source/api/diffpy.structure.rst

@@ -117,4 +117,3 @@ diffpy.structure.sgtbxspacegroups module
     :members:
     :undoc-members:
     :show-inheritance:
-

src/diffpy/Structure.py

@@ -29,6 +29,6 @@
 import diffpy.structure._legacy_importer
 
 # replace this module with the new one
-sys.modules['diffpy.Structure'] = diffpy.structure
+sys.modules["diffpy.Structure"] = diffpy.structure
 
 # End of file

src/diffpy/__init__.py

@@ -21,4 +21,3 @@
 __path__ = extend_path(__path__, __name__)
 
 # End of file
-

src/diffpy/structure/__init__.py

@@ -27,12 +27,11 @@
 
 # Interface definitions ------------------------------------------------------
 
-from diffpy.structure.structureerrors import (StructureFormatError,
-        LatticeError, SymmetryError)
 from diffpy.structure.atom import Atom
 from diffpy.structure.lattice import Lattice
-from diffpy.structure.structure import Structure
 from diffpy.structure.pdffitstructure import PDFFitStructure
+from diffpy.structure.structure import Structure
+from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
 
 # obtain version information
 
@@ -43,7 +42,8 @@
 
 # top level routines
 
-def loadStructure(filename, fmt='auto', **kw):
+
+def loadStructure(filename, fmt="auto", **kw):
     """
     Load new structure object from the specified file.
 
@@ -69,13 +69,14 @@ def loadStructure(filename, fmt='auto', **kw):
         and 'discus' formats.
     """
     from diffpy.structure.parsers import getParser
+
     p = getParser(fmt, **kw)
     rv = p.parseFile(filename)
     return rv
 
+
 # silence pyflakes checker
-assert (StructureFormatError and
-        LatticeError and SymmetryError)
+assert StructureFormatError and LatticeError and SymmetryError
 assert Atom
 assert Lattice
 assert Structure