add pyproject.toml in the top directory to run pre-commit

Author: stevenhua0320

diffpy/srmise/applications/extract.py

@@ -149,9 +149,7 @@ def main():
         "--pf",
         dest="peakfunction",
         metavar="PF",
-        help="Fit peak function PF defined in "
-        "diffpy.srmise.peaks, e.g. "
-        "'GaussianOverR(maxwidth=0.7)'",
+        help="Fit peak function PF defined in " "diffpy.srmise.peaks, e.g. " "'GaussianOverR(maxwidth=0.7)'",
     )
     parser.add_option(
         "--cres",
@@ -230,34 +228,30 @@ def main():
         dest="bpoly0",
         type="string",
         metavar="a0[c]",
-        help="Use constant baseline given by y=a0. "
-        "Append 'c' to make parameter constant.",
+        help="Use constant baseline given by y=a0. " "Append 'c' to make parameter constant.",
     )
     group.add_option(
         "--bpoly1",
         dest="bpoly1",
         type="string",
         nargs=2,
         metavar="a1[c] a0[c]",
-        help="Use baseline given by y=a1*x + a0.  Append 'c' to "
-        "make parameter constant.",
+        help="Use baseline given by y=a1*x + a0.  Append 'c' to " "make parameter constant.",
     )
     group.add_option(
         "--bpoly2",
         dest="bpoly2",
         type="string",
         nargs=3,
         metavar="a2[c] a1[c] a0[c]",
-        help="Use baseline given by y=a2*x^2+a1*x + a0.  Append "
-        "'c' to make parameter constant.",
+        help="Use baseline given by y=a2*x^2+a1*x + a0.  Append " "'c' to make parameter constant.",
     )
     group.add_option(
         "--bseq",
         dest="bseq",
         type="string",
         metavar="FILE",
-        help="Use baseline interpolated from x,y values in FILE. "
-        "This baseline has no free parameters.",
+        help="Use baseline interpolated from x,y values in FILE. " "This baseline has no free parameters.",
     )
     group.add_option(
         "--bspherical",
@@ -343,9 +337,7 @@ def main():
         metavar="FILE",
         help="Save result of extraction to FILE (.srmise " "format).",
     )
-    group.add_option(
-        "--plot", "-p", action="store_true", dest="plot", help="Plot extracted peaks."
-    )
+    group.add_option("--plot", "-p", action="store_true", dest="plot", help="Plot extracted peaks.")
     group.add_option(
         "--liveplot",
         "-l",
@@ -362,9 +354,7 @@ def main():
     )
     parser.add_option_group(group)
 
-    group = OptionGroup(
-        parser, "Verbosity Options", "Control detail printed to console."
-    )
+    group = OptionGroup(parser, "Verbosity Options", "Control detail printed to console.")
     group.add_option(
         "--informative",
         "-i",
@@ -435,9 +425,7 @@ def main():
             options.peakfunction = eval("peaks." + options.peakfunction)
         except Exception as err:
             print(err)
-            print(
-                "Could not create peak function '%s'. Exiting." % options.peakfunction
-            )
+            print("Could not create peak function '%s'. Exiting." % options.peakfunction)
             return
 
     if options.modelevaluator is not None:
@@ -447,9 +435,7 @@ def main():
             options.modelevaluator = eval("modelevaluators." + options.modelevaluator)
         except Exception as err:
             print(err)
-            print(
-                "Could not find ModelEvaluator '%s'. Exiting." % options.modelevaluator
-            )
+            print("Could not find ModelEvaluator '%s'. Exiting." % options.modelevaluator)
             return
 
     if options.bcrystal is not None:
@@ -534,9 +520,7 @@ def main():
         if options.rng is not None:
             pdict["rng"] = list(options.rng)
         if options.qmax is not None:
-            pdict["qmax"] = (
-                options.qmax if options.qmax == "automatic" else float(options.qmax)
-            )
+            pdict["qmax"] = options.qmax if options.qmax == "automatic" else float(options.qmax)
         if options.nyquist is not None:
             pdict["nyquist"] = options.nyquist
         if options.supersample is not None:
@@ -624,10 +608,7 @@ def _format_text(self, text):
         # the above is still the same
         bits = text.split("\n")
         formatted_bits = [
-            textwrap.fill(
-                bit, text_width, initial_indent=indent, subsequent_indent=indent
-            )
-            for bit in bits
+            textwrap.fill(bit, text_width, initial_indent=indent, subsequent_indent=indent) for bit in bits
         ]
         result = "\n".join(formatted_bits) + "\n"
         return result
@@ -665,9 +646,7 @@ def format_option(self, option):
                 help_lines.extend(textwrap.wrap(para, self.help_width))
             # Everything is the same after here
             result.append("%*s%s\n" % (indent_first, "", help_lines[0]))
-            result.extend(
-                ["%*s%s\n" % (self.help_position, "", line) for line in help_lines[1:]]
-            )
+            result.extend(["%*s%s\n" % (self.help_position, "", line) for line in help_lines[1:]])
         elif opts[-1] != "\n":
             result.append("\n")
         return "".join(result)

diffpy/srmise/applications/plot.py

@@ -194,9 +194,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
         x = ppe.x[rangeslice]
         y = ppe.y[rangeslice]
         dy = ppe.effective_dy[rangeslice]
-        mcluster = ModelCluster(
-            ppe.initial_peaks, ppe.baseline, x, y, dy, None, ppe.error_method, ppe.pf
-        )
+        mcluster = ModelCluster(ppe.initial_peaks, ppe.baseline, x, y, dy, None, ppe.error_method, ppe.pf)
         ext = mcluster
     else:
         ext = ppe.extracted
@@ -255,9 +253,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
     # Define the various data which will be plotted
     r = ext.r_cluster
     dr = (r[-1] - r[0]) / len(r)
-    rexpand = np.concatenate(
-        (np.arange(r[0] - dr, xlo, -dr)[::-1], r, np.arange(r[-1] + dr, xhi + dr, dr))
-    )
+    rexpand = np.concatenate((np.arange(r[0] - dr, xlo, -dr)[::-1], r, np.arange(r[-1] + dr, xhi + dr, dr)))
     rfine = np.arange(r[0], r[-1], 0.1 * dr)
     gr_obs = np.array(resample(ppe.x, ppe.y, rexpand)) * scale
     # gr_fit = resample(r, ext.value(), rfine)
@@ -295,21 +291,10 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
         max_res = 0.0
 
     # Derive various y limits based on all the offsets
-    rel_height = (
-        100.0
-        - top_offset
-        - dg_height
-        - cmp_height
-        - datatop_offset
-        - databottom_offset
-        - bottom_offset
-    )
+    rel_height = 100.0 - top_offset - dg_height - cmp_height - datatop_offset - databottom_offset - bottom_offset
     abs_height = 100 * ((max_gr - min_gr) + (max_res - min_res)) / rel_height
 
-    yhi = (
-        max_gr
-        + (top_offset + dg_height + cmp_height + datatop_offset) * abs_height / 100
-    )
+    yhi = max_gr + (top_offset + dg_height + cmp_height + datatop_offset) * abs_height / 100
     ylo = yhi - abs_height
 
     yhi = kwds.get("yhi", yhi)
@@ -353,13 +338,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
 
     # Remove labels above where insets begin
     # ax_data.yaxis.set_ticklabels([str(int(loc)) for loc in ax_data.yaxis.get_majorticklocs() if loc < datatop])
-    ax_data.yaxis.set_ticks(
-        [
-            loc
-            for loc in ax_data.yaxis.get_majorticklocs()
-            if (loc < datatop and loc >= ylo)
-        ]
-    )
+    ax_data.yaxis.set_ticks([loc for loc in ax_data.yaxis.get_majorticklocs() if (loc < datatop and loc >= ylo)])
 
     # Dataset label
     if datalabel is not None:
@@ -378,9 +357,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
 
     # Create new x axis at bottom edge of compare inset
     ax_data.axis["top"].set_visible(False)
-    ax_data.axis["newtop"] = ax_data.new_floating_axis(
-        0, datatop, axis_direction="bottom"
-    )  # "top" bugged?
+    ax_data.axis["newtop"] = ax_data.new_floating_axis(0, datatop, axis_direction="bottom")  # "top" bugged?
     ax_data.axis["newtop"].toggle(all=False, ticks=True)
     ax_data.axis["newtop"].major_ticks.set_tick_out(True)
     ax_data.axis["newtop"].minor_ticks.set_tick_out(True)
@@ -399,9 +376,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
         transform=ax_data.transAxes,
     )
     labeldict[fig] = newylabel  # so we can find the correct text object
-    fig.canvas.mpl_connect(
-        "draw_event", on_draw
-    )  # original label invisibility and updating
+    fig.canvas.mpl_connect("draw_event", on_draw)  # original label invisibility and updating
 
     # Compare extracted (and ideal, if provided) peak positions clearly.
     if cmp_height > 0:
@@ -610,15 +585,9 @@ def main():
         type="int",
         help="Plot given model from set.  Ignored if srmise_file is not a PeakStability file.",
     )
-    parser.add_option(
-        "--show", action="store_true", help="execute pylab.show() blocking call"
-    )
-    parser.add_option(
-        "-o", "--output", type="string", help="save plot to the specified file"
-    )
-    parser.add_option(
-        "--format", type="string", default="eps", help="output format for plot saving"
-    )
+    parser.add_option("--show", action="store_true", help="execute pylab.show() blocking call")
+    parser.add_option("-o", "--output", type="string", help="save plot to the specified file")
+    parser.add_option("--format", type="string", default="eps", help="output format for plot saving")
     parser.allow_interspersed_args = True
     opts, args = parser.parse_args(sys.argv[1:])
 
@@ -636,9 +605,7 @@ def main():
             try:
                 toplot.load(filename)
             except Exception:
-                print(
-                    "File '%s' is not a .srmise or PeakStability data file." % filename
-                )
+                print("File '%s' is not a .srmise or PeakStability data file." % filename)
                 return
 
     if opts.model is not None:

diffpy/srmise/basefunction.py

@@ -116,21 +116,12 @@ def __init__(
 
         # Check validity of default_formats
         self.default_formats = default_formats
-        if not (
-            "default_input" in self.default_formats
-            and "default_output" in self.default_formats
-        ):
-            emsg = (
-                "Argument default_formats must specify 'default_input' "
-                + "and 'default_output' as keys."
-            )
+        if not ("default_input" in self.default_formats and "default_output" in self.default_formats):
+            emsg = "Argument default_formats must specify 'default_input' " + "and 'default_output' as keys."
             raise ValueError(emsg)
         for f in self.default_formats.values():
             if not f in self.parformats:
-                emsg = (
-                    "Keys of argument default_formats must map to a "
-                    + "value within argument parformats."
-                )
+                emsg = "Keys of argument default_formats must map to a " + "value within argument parformats."
                 raise ValueError()
 
         # Set metadictionary
@@ -195,10 +186,7 @@ def jacobian(self, p, r, rng=None):
               previously calculated values instead.
         """
         if self is not p._owner:
-            emsg = (
-                "Argument 'p' must be evaluated by the BaseFunction "
-                + "subclass which owns it."
-            )
+            emsg = "Argument 'p' must be evaluated by the BaseFunction " + "subclass which owns it."
             raise ValueError(emsg)
 
         # normally r will be a sequence, but also allow single numeric values
@@ -241,18 +229,12 @@ def transform_derivatives(self, pars, in_format=None, out_format=None):
             out_format = self.default_formats["default_input"]
 
         if not in_format in self.parformats:
-            raise ValueError(
-                "Argument 'in_format' must be one of %s." % self.parformats
-            )
+            raise ValueError("Argument 'in_format' must be one of %s." % self.parformats)
         if not out_format in self.parformats:
-            raise ValueError(
-                "Argument 'out_format' must be one of %s." % self.parformats
-            )
+            raise ValueError("Argument 'out_format' must be one of %s." % self.parformats)
         if in_format == out_format:
             return np.identity(self.npars)
-        return self._transform_derivativesraw(
-            pars, in_format=in_format, out_format=out_format
-        )
+        return self._transform_derivativesraw(pars, in_format=in_format, out_format=out_format)
 
     def transform_parameters(self, pars, in_format=None, out_format=None):
         """Return new sequence with pars converted from in_format to out_format.
@@ -282,18 +264,12 @@ def transform_parameters(self, pars, in_format=None, out_format=None):
             out_format = self.default_formats["default_input"]
 
         if not in_format in self.parformats:
-            raise ValueError(
-                "Argument 'in_format' must be one of %s." % self.parformats
-            )
+            raise ValueError("Argument 'in_format' must be one of %s." % self.parformats)
         if not out_format in self.parformats:
-            raise ValueError(
-                "Argument 'out_format' must be one of %s." % self.parformats
-            )
+            raise ValueError("Argument 'out_format' must be one of %s." % self.parformats)
         # if in_format == out_format:
         #    return pars
-        return self._transform_parametersraw(
-            pars, in_format=in_format, out_format=out_format
-        )
+        return self._transform_parametersraw(pars, in_format=in_format, out_format=out_format)
 
     def value(self, p, r, rng=None):
         """Calculate value of ModelPart over r, possibly restricted by range.
@@ -307,10 +283,7 @@ def value(self, p, r, rng=None):
               previously calculated values instead.
         """
         if self is not p._owner:
-            emsg = (
-                "Argument 'p' must be evaluated by the BaseFunction "
-                + "subclass which owns it."
-            )
+            emsg = "Argument 'p' must be evaluated by the BaseFunction " + "subclass which owns it."
             raise ValueError(emsg)
 
         # normally r will be a sequence, but also allow single numeric values

diffpy/srmise/baselines/arbitrary.py

@@ -95,9 +95,7 @@ def __init__(self, npars, valuef, jacobianf=None, estimatef=None, Cache=None):
         metadict["valuef"] = (valuef, repr)
         metadict["jacobianf"] = (jacobianf, repr)
         metadict["estimatef"] = (estimatef, repr)
-        BaselineFunction.__init__(
-            self, parameterdict, formats, default_formats, metadict, None, Cache
-        )
+        BaselineFunction.__init__(self, parameterdict, formats, default_formats, metadict, None, Cache)
 
     #### Methods required by BaselineFunction ####
 
@@ -173,17 +171,13 @@ def _transform_parametersraw(self, pars, in_format, out_format):
         if in_format == "internal":
             pass
         else:
-            raise ValueError(
-                "Argument 'in_format' must be one of %s." % self.parformats
-            )
+            raise ValueError("Argument 'in_format' must be one of %s." % self.parformats)
 
         # Convert to specified output format from "internal" format.
         if out_format == "internal":
             pass
         else:
-            raise ValueError(
-                "Argument 'out_format' must be one of %s." % self.parformats
-            )
+            raise ValueError("Argument 'out_format' must be one of %s." % self.parformats)
         return temp
 
     def _valueraw(self, pars, r):

diffpy/srmise/baselines/base.py

@@ -83,9 +83,7 @@ def __init__(
               additional functionality.
         Cache: A class (not instance) which implements caching of BaseFunction
                evaluations."""
-        BaseFunction.__init__(
-            self, parameterdict, parformats, default_formats, metadict, base, Cache
-        )
+        BaseFunction.__init__(self, parameterdict, parformats, default_formats, metadict, base, Cache)
 
     #### "Virtual" class methods ####