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

sbillinge · Jul 23, 2024 · Jul 22, 2024 · Jul 22, 2024 · Jul 22, 2024 · 6eb7215b1032d5911127e346e58613a532733993
commit 6eb7215b1032d5911127e346e58613a532733993
diff --git a/conda-recipe/expandpdfguibase.py b/conda-recipe/expandpdfguibase.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import sys
+
 from pkg_resources import Requirement, resource_filename
 
 pkg = Requirement.parse("diffpy.pdfgui")

diff --git a/devutils/makesdist b/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))
 

diff --git a/setup.py b/setup.py
@@ -11,7 +11,8 @@
 import os
 import re
 import sys
-from setuptools import setup, find_packages
+
+from setuptools import find_packages, setup
 
 # Use this version when git data are not available, like in git zip archive.
 # Update when tagging a new release.
@@ -28,7 +29,7 @@
 
 
 def gitinfo():
-    from subprocess import Popen, PIPE
+    from subprocess import PIPE, Popen
 
     kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
     proc = Popen(["git", "describe", "--tags", "--match=v[[:digit:]]*"], **kw)
@@ -67,10 +68,7 @@ def getversioncfg():
     cp = RawConfigParser()
     cp.read(versioncfgfile)
     d = cp.defaults()
-    rewrite = not d or (
-        g["commit"]
-        and (g["version"] != d.get("version") or g["commit"] != d.get("commit"))
-    )
+    rewrite = not d or (g["commit"] and (g["version"] != d.get("version") or g["commit"] != d.get("commit")))
     if rewrite:
         cp.set("DEFAULT", "version", g["version"])
         cp.set("DEFAULT", "commit", g["commit"])

diff --git a/src/diffpy/pdfgui/applications/pdfgui.py b/src/diffpy/pdfgui/applications/pdfgui.py
@@ -34,9 +34,9 @@
 
 from __future__ import print_function
 
-import sys
-import os
 import getopt
+import os
+import sys
 
 
 def usage():

diff --git a/src/diffpy/pdfgui/control/calculation.py b/src/diffpy/pdfgui/control/calculation.py
@@ -19,11 +19,13 @@
 import copy
 import math
 
-from diffpy.pdfgui.control.controlerrors import ControlConfigError
-from diffpy.pdfgui.control.controlerrors import ControlKeyError
-from diffpy.pdfgui.control.controlerrors import ControlValueError
+from diffpy.pdfgui.control.controlerrors import (
+    ControlConfigError,
+    ControlKeyError,
+    ControlValueError,
+)
 from diffpy.pdfgui.control.pdfcomponent import PDFComponent
-from diffpy.pdfgui.utils import safeCPickleDumps, pickle_loads
+from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps
 
 
 class Calculation(PDFComponent):

diff --git a/src/diffpy/pdfgui/control/constraint.py b/src/diffpy/pdfgui/control/constraint.py
@@ -17,8 +17,8 @@
 constraints will be stored in { variable : constraint } dictionary
 """
 
-import re
 import math
+import re
 
 from diffpy.pdfgui.control.controlerrors import ControlSyntaxError
 
@@ -135,9 +135,7 @@ def __setattr__(self, name, value):
             raise ControlSyntaxError(message)
         # few more checks of the formula:
         if newformula.find("**") != -1:
-            emsg = (
-                "invalid constraint formula '{}', " "operator '**' not supported."
-            ).format(newformula)
+            emsg = ("invalid constraint formula '{}', " "operator '**' not supported.").format(newformula)
             raise ControlSyntaxError(emsg)
         # checks checked
         self.__dict__["formula"] = newformula

diff --git a/src/diffpy/pdfgui/control/fitdataset.py b/src/diffpy/pdfgui/control/fitdataset.py
@@ -17,11 +17,12 @@
 """
 
 import copy
+
 import numpy
 
-from diffpy.pdfgui.control.pdfdataset import PDFDataSet
-from diffpy.pdfgui.control.parameter import Parameter
 from diffpy.pdfgui.control.controlerrors import ControlStatusError
+from diffpy.pdfgui.control.parameter import Parameter
+from diffpy.pdfgui.control.pdfdataset import PDFDataSet
 
 
 class FitDataSet(PDFDataSet):
@@ -112,9 +113,7 @@ def getYNames(self):
 
         returns list of strings
         """
-        ynames = ["Gobs", "Gcalc", "Gdiff", "Gtrunc", "dGcalc", "crw"] + list(
-            self.constraints.keys()
-        )
+        ynames = ["Gobs", "Gcalc", "Gdiff", "Gtrunc", "dGcalc", "crw"] + list(self.constraints.keys())
         return ynames
 
     def getXNames(self):
@@ -321,10 +320,7 @@ def writeCalcStr(self):
         Gdiff = self.Gdiff
         drcalc = 0.0
         for i in range(len(self.rcalc)):
-            lines.append(
-                "%g %g %.1f %g %g"
-                % (self.rcalc[i], self.Gcalc[i], drcalc, self.dGcalc[i], Gdiff[i])
-            )
+            lines.append("%g %g %.1f %g %g" % (self.rcalc[i], self.Gcalc[i], drcalc, self.dGcalc[i], Gdiff[i]))
         # lines are ready here
         datastring = "\n".join(lines) + "\n"
         return datastring
@@ -636,9 +632,7 @@ def _set_fitrmin(self, value):
         self._fitrmin = float(value)
         return
 
-    fitrmin = property(
-        _get_fitrmin, _set_fitrmin, doc="Lower boundary for simulated PDF curve."
-    )
+    fitrmin = property(_get_fitrmin, _set_fitrmin, doc="Lower boundary for simulated PDF curve.")
 
     # fitrmax
 
@@ -650,9 +644,7 @@ def _set_fitrmax(self, value):
         self._fitrmax = float(value)
         return
 
-    fitrmax = property(
-        _get_fitrmax, _set_fitrmax, doc="Upper boundary for simulated PDF curve."
-    )
+    fitrmax = property(_get_fitrmax, _set_fitrmax, doc="Upper boundary for simulated PDF curve.")
 
     # fitrstep
 
@@ -664,9 +656,7 @@ def _set_fitrstep(self, value):
         self._fitrstep = float(value)
         return
 
-    fitrstep = property(
-        _get_fitrstep, _set_fitrstep, doc="R-step used for simulated PDF curve."
-    )
+    fitrstep = property(_get_fitrstep, _set_fitrstep, doc="R-step used for simulated PDF curve.")
 
     # rcalc
 
@@ -707,9 +697,7 @@ def _set_dGcalc(self, value):
         self._dGcalc = value
         return
 
-    dGcalc = property(
-        _get_dGcalc, _set_dGcalc, doc="List of standard deviations of Gcalc."
-    )
+    dGcalc = property(_get_dGcalc, _set_dGcalc, doc="List of standard deviations of Gcalc.")
 
     # Gtrunc
 
@@ -757,9 +745,7 @@ def _get_Gdiff(self):
             rv = []
         return rv
 
-    Gdiff = property(
-        _get_Gdiff, doc="Difference between observed and calculated PDF on rcalc grid."
-    )
+    Gdiff = property(_get_Gdiff, doc="Difference between observed and calculated PDF on rcalc grid.")
 
     # crw
     def _get_crw(self):

diff --git a/src/diffpy/pdfgui/control/fitstructure.py b/src/diffpy/pdfgui/control/fitstructure.py
@@ -18,12 +18,13 @@
 
 import copy
 import re
+
 import numpy
 
-from diffpy.pdfgui.control.pdfstructure import PDFStructure
 from diffpy.pdfgui.control.constraint import Constraint
-from diffpy.pdfgui.control.parameter import Parameter
 from diffpy.pdfgui.control.controlerrors import ControlTypeError, ControlValueError
+from diffpy.pdfgui.control.parameter import Parameter
+from diffpy.pdfgui.control.pdfstructure import PDFStructure
 from diffpy.structure import Atom
 
 
@@ -309,12 +310,7 @@ def expandSuperCell(self, mno):
         # back to business
         acd = self._popAtomConstraints()
         mnofloats = numpy.array(mno[:3], dtype=float)
-        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])]
         # build a list of new atoms
         newatoms = []
         for a in self.initial:
@@ -389,9 +385,7 @@ def getSpaceGroupList(self):
                 existing_names[sg.short_name] = True
             # sort by International Tables number, stay compatible with 2.3
             n_sg = [(sg.number % 1000, sg) for sg in unique_named_list]
-            n_sg = sorted(
-                n_sg, key=lambda x: x[0]
-            )  # sort by the first element of tuple.
+            n_sg = sorted(n_sg, key=lambda x: x[0])  # sort by the first element of tuple.
             FitStructure.sorted_standard_space_groups = [sg for n, sg in n_sg]
         sglist = list(FitStructure.sorted_standard_space_groups)
         if self.custom_spacegroup:
@@ -438,9 +432,7 @@ def expandAsymmetricUnit(self, spacegroup, indices, sgoffset=[0, 0, 0]):
         coreatoms = [self.initial[i] for i in ruindices]
         corepos = [a.xyz for a in coreatoms]
         coreUijs = [a.U for a in coreatoms]
-        eau = ExpandAsymmetricUnit(
-            spacegroup, corepos, coreUijs, sgoffset=sgoffset, eps=self.symposeps
-        )
+        eau = ExpandAsymmetricUnit(spacegroup, corepos, coreUijs, sgoffset=sgoffset, eps=self.symposeps)
         # build a nested list of new atoms:
         newatoms = []
         for i in range(len(coreatoms)):
@@ -469,9 +461,7 @@ def expandAsymmetricUnit(self, spacegroup, indices, sgoffset=[0, 0, 0]):
         self._restoreAtomConstraints(acd)
         return
 
-    def applySymmetryConstraints(
-        self, spacegroup, indices, posflag, Uijflag, sgoffset=[0, 0, 0]
-    ):
+    def applySymmetryConstraints(self, spacegroup, indices, posflag, Uijflag, sgoffset=[0, 0, 0]):
         """Generate symmetry constraints for positions and thermal factors.
         Both positions and thermal factors may get corrected to reflect
         space group symmetry.  Old positional and thermal constraints get
@@ -511,9 +501,7 @@ def applySymmetryConstraints(
         selatoms = [self.initial[i] for i in uindices]
         selpos = [a.xyz for a in selatoms]
         selUijs = [a.U for a in selatoms]
-        symcon = SymmetryConstraints(
-            spacegroup, selpos, selUijs, sgoffset=sgoffset, eps=self.symposeps
-        )
+        symcon = SymmetryConstraints(spacegroup, selpos, selUijs, sgoffset=sgoffset, eps=self.symposeps)
         # deal with positions
         if posflag:
             # fix positions:
@@ -762,8 +750,8 @@ def load(self, z, subpath):
         subpath -- path to its own storage within project file
         """
         # subpath = projname/fitname/structure/myname/
-        from diffpy.pdfgui.utils import asunicode
         from diffpy.pdfgui.control.pdfguicontrol import CtrlUnpickler
+        from diffpy.pdfgui.utils import asunicode
 
         subs = subpath.split("/")
         rootDict = z.fileTree[subs[0]][subs[1]][subs[2]][subs[3]]

diff --git a/src/diffpy/pdfgui/control/fitting.py b/src/diffpy/pdfgui/control/fitting.py
@@ -18,23 +18,25 @@
 import threading
 import time
 
+from diffpy.pdfgui.control.controlerrors import (
+    ControlError,
+    ControlStatusError,
+    ControlValueError,
+)
 from diffpy.pdfgui.control.organizer import Organizer
-from diffpy.pdfgui.control.controlerrors import ControlError
-from diffpy.pdfgui.control.controlerrors import ControlStatusError
-from diffpy.pdfgui.control.controlerrors import ControlValueError
-from diffpy.pdfgui.utils import safeCPickleDumps, pickle_loads
+from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps
 
 # helper routines to deal with PDFfit2 exceptions
 
 
 def getEngineExceptions():
     """Return a tuple of possible exceptions from diffpy.pdffit2.pdffit2."""
     from diffpy.pdffit2.pdffit2 import (
-        dataError,
-        unassignedError,
+        calculationError,
         constraintError,
+        dataError,
         structureError,
-        calculationError,
+        unassignedError,
     )
 
     engine_exceptions = (
@@ -212,9 +214,7 @@ def load(self, z, subpath):
 
             self.parameters = CtrlUnpickler.loads(z.read(subpath + "parameters"))
         if "steps" in rootDict:
-            self.itemIndex, self.dataNameDict, self.snapshots = pickle_loads(
-                z.read(subpath + "steps")
-            )
+            self.itemIndex, self.dataNameDict, self.snapshots = pickle_loads(z.read(subpath + "steps"))
         if "result" in rootDict:
             self.rw, self.res = pickle_loads(z.read(subpath + "result"))
 
@@ -582,9 +582,7 @@ def close(self, force=False):
                 #      way while user choose to stop forcefully
         else:
             if self.isThreadRunning():
-                raise ControlStatusError(
-                    "Fitting: Fitting %s is still running" % self.name
-                )
+                raise ControlStatusError("Fitting: Fitting %s is still running" % self.name)
             if self.thread is not None:
                 self.thread.join()