fix python2 to python3 to make pre-commit black hook work (#16)

* fix python2 to python3 to make pre-commit black hook work * add pyproject.toml and pre-commit work
diffpy · Jul 29, 2024 · fd65cf6 · fd65cf6
1 parent 75e5111
commit fd65cf6
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Showing 31 changed files with 1,035 additions and 1,093 deletions.
diff --git a/devutils/makesdist b/devutils/makesdist
@@ -17,11 +17,11 @@ sys.path.insert(0, BASEDIR)
 from setup import versiondata
 timestamp = versiondata.getint('DEFAULT', 'timestamp')
 
-print 'Run "setup.py sdist --formats=tar"',
+print('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)
-print "[done]"
+print("[done]")
 
 tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
 
@@ -36,8 +36,8 @@ def fixtarinfo(tinfo):
     return tinfo
 
 
-print 'Filter %s --> %s.gz' % (2 * (os.path.basename(tarname),)),
+print('Filter %s --> %s.gz' % (2 * (os.path.basename(tarname),)),)
 for ti in tfin:
     tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
 os.remove(tarname)
-print "[done]"
+print("[done]")
diff --git a/devutils/prep.py b/devutils/prep.py
@@ -8,6 +8,8 @@
 
 __basedir__ = os.getcwdu()
 
+from numpy.compat import unicode
+
 # Example imports
 
 
@@ -18,20 +20,21 @@ def __init__(self):
 
     def test(self, call, *args, **kwds):
         m = sys.modules[call.__module__]
-        testname = m.__name__+'.'+call.__name__
+        testname = m.__name__ + "." + call.__name__
         path = os.path.dirname(m.__file__)
         os.chdir(path)
         try:
             call(*args, **kwds)
-            self.messages.append("%s: success" %testname)
-        except Exception, e:
-            self.messages.append("%s: error, details below.\n%s" %(testname, e))
+            self.messages.append("%s: success" % testname)
+        except Exception as e:
+            self.messages.append("%s: error, details below.\n%s" % (testname, e))
         finally:
             os.chdir(__basedir__)
 
     def report(self):
-        print '==== Results of Tests ===='
-        print '\n'.join(self.messages)
+        print("==== Results of Tests ====")
+        print("\n".join(self.messages))
+
 
 def scrubeol(directory, filerestr):
     """Use unix-style endlines for files in directory matched by regex string.
@@ -50,11 +53,11 @@ def scrubeol(directory, filerestr):
         text = unicode(original.read())
         original.close()
 
-        updated = io.open(f, 'w', newline='\n')
+        updated = io.open(f, "w", newline="\n")
         updated.write(text)
         updated.close()
 
-        print "Updated %s to unix-style endlines." %f
+        print("Updated %s to unix-style endlines." % f)
 
 
 def rm(directory, filerestr):
@@ -72,14 +75,13 @@ def rm(directory, filerestr):
     for f in files:
         os.remove(f)
 
-        print "Deleted %s." %f
-
+        print("Deleted %s." % f)
 
 
 if __name__ == "__main__":
 
     # Temporarily add examples to path
-    lib_path = os.path.abspath(os.path.join('..','doc','examples'))
+    lib_path = os.path.abspath(os.path.join("..", "doc", "examples"))
     sys.path.append(lib_path)
 
     # Delete existing files that don't necessarily have a fixed name.
@@ -88,14 +90,16 @@ def rm(directory, filerestr):
 
     ### Testing examples
     examples = Test()
-    test_names = ["extract_single_peak",
-                  "parameter_summary",
-                  "fit_initial",
-                  "query_results",
-                  "multimodel_known_dG1",
-                  "multimodel_known_dG2",
-                  "multimodel_unknown_dG1",
-                  "multimodel_unknown_dG2"]
+    test_names = [
+        "extract_single_peak",
+        "parameter_summary",
+        "fit_initial",
+        "query_results",
+        "multimodel_known_dG1",
+        "multimodel_known_dG2",
+        "multimodel_unknown_dG1",
+        "multimodel_unknown_dG2",
+    ]
 
     test_modules = []
     for test in test_names:
@@ -107,7 +111,7 @@ def rm(directory, filerestr):
     examples.report()
 
     ### Convert output of example files to Unix-style endlines for sdist.
-    if os.linesep != '\n':
-        print "==== Scrubbing Endlines ===="
+    if os.linesep != "\n":
+        print("==== Scrubbing Endlines ====")
         # All *.srmise and *.pwa files in examples directory.
         scrubeol("../doc/examples/output", r".*(\.srmise|\.pwa)")
diff --git a/diffpy/srmise/applications/extract.py b/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)

diff --git a/diffpy/srmise/applications/plot.py b/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: