fix python2 to python3 to make pre-commit black hook work

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]")

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)")

diffpy/srmise/baselines/arbitrary.py

@@ -17,12 +17,14 @@
 import numpy as np
 
 import diffpy.srmise.srmiselog
+from diffpy.srmise.baselines import Polynomial
 from diffpy.srmise.baselines.base import BaselineFunction
 from diffpy.srmise.srmiseerrors import SrMiseEstimationError
 
 logger = logging.getLogger("diffpy.srmise")
 
-class Arbitrary (BaselineFunction):
+
+class Arbitrary(BaselineFunction):
     """Methods for evaluating a baseline from an arbitrary function.
 
     Supports baseline calculations with arbitrary functions.  These functions,
@@ -64,10 +66,10 @@ def __init__(self, npars, valuef, jacobianf=None, estimatef=None, Cache=None):
         # Define parameterdict
         # e.g. {"a_0":0, "a_1":1, "a_2":2, "a_3":3} if npars is 4.
         parameterdict = {}
-        for d in range(self.testnpars+1):
-            parameterdict["a_"+str(d)] = d
-        formats = ['internal']
-        default_formats = {'default_input':'internal', 'default_output':'internal'}
+        for d in range(self.testnpars + 1):
+            parameterdict["a_" + str(d)] = d
+        formats = ["internal"]
+        default_formats = {"default_input": "internal", "default_output": "internal"}
 
         # Check that the provided functions are at least callable
         if valuef is None or callable(valuef):
@@ -93,7 +95,9 @@ 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 ####
 
@@ -114,9 +118,8 @@ def estimate_parameters(self, r, y):
         # TODO: check that estimatef returns something proper?
         try:
             return self.estimatef(r, y)
-        except Exception, e:
-            emsg = "Error within estimation routine provided to Arbitrary:\n"+\
-                   str(e)
+        except Exception as e:
+            emsg = "Error within estimation routine provided to Arbitrary:\n" + str(e)
             raise SrMiseEstimationError(emsg)
 
     def _jacobianraw(self, pars, r, free):
@@ -137,10 +140,10 @@ def _jacobianraw(self, pars, r, free):
                 emsg = "No jacobian routine provided to Arbitrary."
                 raise NotImplementedError(emsg)
         if len(pars) != self.npars:
-            emsg = "Argument pars must have "+str(self.npars)+" elements."
+            emsg = "Argument pars must have " + str(self.npars) + " elements."
             raise ValueError(emsg)
         if len(free) != self.npars:
-            emsg = "Argument free must have "+str(self.npars)+" elements."
+            emsg = "Argument free must have " + str(self.npars) + " elements."
             raise ValueError(emsg)
 
         # Allow an arbitrary function without a Jacobian provided act as
@@ -149,7 +152,7 @@ def _jacobianraw(self, pars, r, free):
         # large performance implications if all other functions used while
         # fitting a function define a Jacobian.
         if nfree == 0:
-            return [None for p in range(len(par))]
+            return [None for p in range(len(pars))]
 
         # TODO: check that jacobianf returns something proper?
         return self.jacobianf(pars, r, free)
@@ -170,15 +173,17 @@ 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):
@@ -192,7 +197,7 @@ def _valueraw(self, pars, r):
             ...
         r: sequence or scalar over which pars is evaluated"""
         if len(pars) != self.npars:
-            emsg = "Argument pars must have "+str(self.npars)+" elements."
+            emsg = "Argument pars must have " + str(self.npars) + " elements."
             raise ValueError(emsg)
 
         # TODO: check that valuef returns something proper?
@@ -201,21 +206,22 @@ def _valueraw(self, pars, r):
     def getmodule(self):
         return __name__
 
-#end of class Polynomial
+
+# end of class Polynomial
 
 # simple test code
-if __name__ == '__main__':
+if __name__ == "__main__":
 
-    f = Polynomial(degree = 3)
+    f = Polynomial(degree=3)
     r = np.arange(5)
     pars = np.array([3, 0, 1, 2])
     free = np.array([True, False, True, True])
-    print f._valueraw(pars, r)
-    print f._jacobianraw(pars, r, free)
+    print(f._valueraw(pars, r))
+    print(f._jacobianraw(pars, r, free))
 
-    f = Polynomial(degree = -1)
+    f = Polynomial(degree=-1)
     r = np.arange(5)
     pars = np.array([])
     free = np.array([])
-    print f._valueraw(pars, r)
-    print f._jacobianraw(pars, r, free)
+    print(f._valueraw(pars, r))
+    print(f._jacobianraw(pars, r, free))

diffpy/srmise/baselines/base.py

@@ -18,6 +18,7 @@
 import diffpy.srmise.srmiselog
 from diffpy.srmise.basefunction import BaseFunction
 from diffpy.srmise.modelparts import ModelPart
+from diffpy.srmise.peaks import Peaks
 from diffpy.srmise.srmiseerrors import *
 
 logger = logging.getLogger("diffpy.srmise")