black autofix

sbillinge · Jun 27, 2025 · Dec 28, 2024 · Dec 28, 2024 · Dec 28, 2024 · Dec 30, 2024
commit 6198d352f84d9babfda3a0e77c93164b79e1dde5
diff --git a/conda-recipe/run_test.py b/conda-recipe/run_test.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
 
 import diffpy.srreal.tests
+
 assert diffpy.srreal.tests.test().wasSuccessful()
diff --git a/devutils/tunePeakPrecision.py b/devutils/tunePeakPrecision.py
@@ -30,11 +30,12 @@
 from diffpy.structure import Structure
 from diffpy.srreal.pdf_ext import PDFCalculator
 import diffpy.pdffit2
+
 # make PdfFit silent
-diffpy.pdffit2.redirect_stdout(open('/dev/null', 'w'))
+diffpy.pdffit2.redirect_stdout(open("/dev/null", "w"))
 
 # define nickel structure data
-nickel_discus_data = '''
+nickel_discus_data = """
 title   Ni
 spcgr   P1
 cell    3.523870,  3.523870,  3.523870, 90.000000, 90.000000, 90.000000
@@ -44,10 +45,10 @@
 NI          0.00000000        0.50000000        0.50000000       0.1000
 NI          0.50000000        0.00000000        0.50000000       0.1000
 NI          0.50000000        0.50000000        0.00000000       0.1000
-'''
+"""
 
 nickel = Structure()
-nickel.readStr(nickel_discus_data, format='discus')
+nickel.readStr(nickel_discus_data, format="discus")
 
 
 def Gpdffit2(qmax):
@@ -59,7 +60,7 @@ def Gpdffit2(qmax):
     """
     # calculate reference data using pdffit2
     pf2 = diffpy.pdffit2.PdfFit()
-    pf2.alloc('X', qmax, 0.0, rmin, rmax, int((rmax - rmin) / rstep + 1))
+    pf2.alloc("X", qmax, 0.0, rmin, rmax, int((rmax - rmin) / rstep + 1))
     pf2.add_structure(nickel)
     pf2.calc()
     rg = numpy.array((pf2.getR(), pf2.getpdf_fit()))
@@ -81,7 +82,7 @@ def Gsrreal(qmax, peakprecision=None):
     pdfcalc._setDoubleAttr("rmax", rmax + rstep * 1e-4)
     pdfcalc._setDoubleAttr("rstep", rstep)
     if peakprecision is not None:
-        pdfcalc._setDoubleAttr('peakprecision', peakprecision)
+        pdfcalc._setDoubleAttr("peakprecision", peakprecision)
     pdfcalc.eval(nickel)
     rg = numpy.array([pdfcalc.rgrid, pdfcalc.pdf])
     return rg
@@ -105,38 +106,39 @@ def comparePDFCalculators(qmax, peakprecision=None):
     t0, t1  -- CPU times used by pdffit2 and PDFCalculator calls
     """
     rv = {}
-    rv['qmax'] = qmax
-    rv['peakprecision'] = (peakprecision is None and
-            PDFCalculator()._getDoubleAttr('peakprecision') or peakprecision)
+    rv["qmax"] = qmax
+    rv["peakprecision"] = (
+        peakprecision is None and PDFCalculator()._getDoubleAttr("peakprecision") or peakprecision
+    )
     ttic = time.clock()
     rg0 = Gpdffit2(qmax)
     ttoc = time.clock()
-    rv['r'] = rg0[0]
-    rv['g0'] = rg0[1]
-    rv['t0'] = ttoc - ttic
+    rv["r"] = rg0[0]
+    rv["g0"] = rg0[1]
+    rv["t0"] = ttoc - ttic
     ttic = time.clock()
     rg1 = Gsrreal(qmax, peakprecision)
     ttoc = time.clock()
-    assert numpy.all(rv['r'] == rg1[0])
-    rv['g1'] = rg1[1]
-    rv['t1'] = ttoc - ttic
-    rv['gdiff'] = rv['g0'] - rv['g1']
-    rv['grmsd'] = numpy.sqrt(numpy.mean(rv['gdiff']**2))
+    assert numpy.all(rv["r"] == rg1[0])
+    rv["g1"] = rg1[1]
+    rv["t1"] = ttoc - ttic
+    rv["gdiff"] = rv["g0"] - rv["g1"]
+    rv["grmsd"] = numpy.sqrt(numpy.mean(rv["gdiff"] ** 2))
     return rv
 
 
 def processCommandLineArguments():
     global qmax, peakprecision, createplot
     argc = len(sys.argv)
-    if set(['-h', '--help']).intersection(sys.argv):
+    if set(["-h", "--help"]).intersection(sys.argv):
         print(__doc__)
         sys.exit()
     if argc > 1:
         qmax = float(sys.argv[1])
     if argc > 2:
         peakprecision = float(sys.argv[2])
     if argc > 3:
-        createplot = sys.argv[3].lower() in ('y', 'yes', '1', 'true')
+        createplot = sys.argv[3].lower() in ("y", "yes", "1", "true")
     return
 
 
@@ -148,37 +150,41 @@ def plotComparison(cmpdata):
     No return value.
     """
     import pylab
+
     pylab.clf()
     pylab.subplot(211)
-    pylab.title('qmax=%(qmax)g  peakprecision=%(peakprecision)g' % cmpdata)
-    pylab.ylabel('G')
-    r = cmpdata['r']
-    g0 = cmpdata['g0']
-    g1 = cmpdata['g1']
-    gdiff = cmpdata['gdiff']
+    pylab.title("qmax=%(qmax)g  peakprecision=%(peakprecision)g" % cmpdata)
+    pylab.ylabel("G")
+    r = cmpdata["r"]
+    g0 = cmpdata["g0"]
+    g1 = cmpdata["g1"]
+    gdiff = cmpdata["gdiff"]
     pylab.plot(r, g0, r, g1)
     pylab.subplot(212)
-    pylab.plot(r, gdiff, 'r')
+    pylab.plot(r, gdiff, "r")
     slope = numpy.sum(r * gdiff) / numpy.sum(r**2)
-    pylab.plot(r, slope * r, '--')
-    pylab.xlabel('r')
-    pylab.ylabel('Gdiff')
-    pylab.title('slope = %g' % slope)
+    pylab.plot(r, slope * r, "--")
+    pylab.xlabel("r")
+    pylab.ylabel("Gdiff")
+    pylab.title("slope = %g" % slope)
     pylab.draw()
     return
 
 
 def main():
     processCommandLineArguments()
     cmpdata = comparePDFCalculators(qmax, peakprecision)
-    print(("qmax = %(qmax)g  pkprec = %(peakprecision)g  " +
-           "grmsd = %(grmsd)g  t0 = %(t0).3f  t1 = %(t1).3f") % cmpdata)
+    print(
+        ("qmax = %(qmax)g  pkprec = %(peakprecision)g  " + "grmsd = %(grmsd)g  t0 = %(t0).3f  t1 = %(t1).3f")
+        % cmpdata
+    )
     if createplot:
         plotComparison(cmpdata)
         import pylab
+
         pylab.show()
     return
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/doc/manual/source/conf.py b/doc/manual/source/conf.py
@@ -19,11 +19,11 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../../..'))
+# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath("../../.."))
 
 # abbreviations
-ab_authors = u'Pavol Juhás, Christopher L. Farrow, Simon J.L. Billinge group'
+ab_authors = "Pavol Juhás, Christopher L. Farrow, Simon J.L. Billinge group"
 
 # -- General configuration -----------------------------------------------------
 
@@ -33,38 +33,39 @@
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.intersphinx',
-    'm2r',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "m2r",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'diffpy.srreal'
-copyright = '%Y, Brookhaven National Laboratory'
+project = "diffpy.srreal"
+copyright = "%Y, Brookhaven National Laboratory"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 from setup import versiondata
-fullversion = versiondata.get('DEFAULT', 'version')
+
+fullversion = versiondata.get("DEFAULT", "version")
 # The short X.Y version.
-version = ''.join(fullversion.split('.post')[:1])
+version = "".join(fullversion.split(".post")[:1])
 # The full version, including alpha/beta/rc tags.
 release = fullversion
 
@@ -75,13 +76,13 @@
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 # today = ''
-today_seconds = versiondata.getint('DEFAULT', 'timestamp')
-today = time.strftime('%B %d, %Y', time.localtime(today_seconds))
+today_seconds = versiondata.getint("DEFAULT", "timestamp")
+today = time.strftime("%B %d, %Y", time.localtime(today_seconds))
 year = today.split()[-1]
 # Else, today_fmt is used as the format for a strftime call.
 # today_fmt = '%B %d, %Y'
 # substitute YEAR in the copyright string
-copyright = copyright.replace('%Y', year)
+copyright = copyright.replace("%Y", year)
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -102,10 +103,10 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-modindex_common_prefix = ['diffpy.srreal']
+modindex_common_prefix = ["diffpy.srreal"]
 
 # Display all warnings for missing links.
 nitpicky = True
@@ -114,14 +115,14 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_py3doc_enhanced_theme'
+html_theme = "sphinx_py3doc_enhanced_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    'collapsiblesidebar' : 'true',
-    'navigation_with_keys' : 'true',
+    "collapsiblesidebar": "true",
+    "navigation_with_keys": "true",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -190,27 +191,24 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'srrealdoc'
+htmlhelp_basename = "srrealdoc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-# 'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-# 'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-# 'preamble': '',
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ('index', 'diffpy.srreal.tex', 'diffpy.srreal Documentation',
-     ab_authors, 'manual'),
+    ("index", "diffpy.srreal.tex", "diffpy.srreal Documentation", ab_authors, "manual"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -238,10 +236,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'diffpy.srreal', 'diffpy.srreal Documentation',
-     ab_authors, 1)
-]
+man_pages = [("index", "diffpy.srreal", "diffpy.srreal Documentation", ab_authors, 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -253,9 +248,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'diffpy.srreal', 'diffpy.srreal Documentation',
-     ab_authors, 'diffpy.srreal', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        "index",
+        "diffpy.srreal",
+        "diffpy.srreal Documentation",
+        ab_authors,
+        "diffpy.srreal",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
@@ -270,6 +271,6 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    'numpy': ('https://docs.scipy.org/doc/numpy', None),
-    'python' : ('https://docs.python.org/3.7', None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "python": ("https://docs.python.org/3.7", None),
 }
diff --git a/examples/compareC60PDFs.py b/examples/compareC60PDFs.py
@@ -11,13 +11,14 @@
 from diffpy.srreal.pdfcalculator import PDFCalculator, DebyePDFCalculator
 
 mydir = os.path.dirname(os.path.abspath(sys.argv[0]))
-buckyfile = os.path.join(mydir, 'datafiles', 'C60bucky.stru')
+buckyfile = os.path.join(mydir, "datafiles", "C60bucky.stru")
 
 # load C60 molecule as a diffpy.structure object
 bucky = Structure(filename=buckyfile)
-cfg = { 'qmax' : 25,
-        'rmin' : 0,
-        'rmax' : 10.001,
+cfg = {
+    "qmax": 25,
+    "rmin": 0,
+    "rmax": 10.001,
 }
 
 # calculate PDF by real-space summation

diff --git a/examples/compareC60PDFs_objcryst.py b/examples/compareC60PDFs_objcryst.py
@@ -12,10 +12,10 @@
 from diffpy.srreal.pdfcalculator import PDFCalculator, DebyePDFCalculator
 
 # load C60 molecule as a diffpy.structure object
-bucky_diffpy = Structure(filename='datafiles/C60bucky.stru')
+bucky_diffpy = Structure(filename="datafiles/C60bucky.stru")
 
 # convert to an ObjCryst molecule
-c60 = Crystal(1, 1, 1, 'P1')
+c60 = Crystal(1, 1, 1, "P1")
 mc60 = Molecule(c60, "C60")
 c60.AddScatterer(mc60)
 # Create the scattering power object for the carbon atoms
@@ -26,10 +26,11 @@
     mc60.AddAtom(a.xyz_cartn[0], a.xyz_cartn[1], a.xyz_cartn[2], sp, cname)
 
 # PDF configuration
-cfg = { 'qmax' : 25,
-        'rmin' : 0,
-        'rmax' : 10.001,
-        'rstep' : 0.05,
+cfg = {
+    "qmax": 25,
+    "rmin": 0,
+    "rmax": 10.001,
+    "rstep": 0.05,
 }
 
 # calculate PDF by real-space summation