Drop some leftover py2 compat

Author: michalsta

src/IsoSpecPy/IsoSpecPy.py

@@ -23,11 +23,6 @@
 from collections import namedtuple, OrderedDict
 import math
 
-try:
-    xrange
-except NameError:
-    xrange = range
-
 regex_pattern = re.compile('([A-Z][a-z]?)(-?[0-9]*)')
 ParsedFormula = namedtuple('ParsedFormula', 'atomCounts masses probs elems')
 
@@ -200,9 +195,9 @@ def __init__(self, formula="",
 
         if get_confs:
             i = 0
-            for j in xrange(self.dimNumber):
+            for j in range(self.dimNumber):
                 newl = []
-                for k in xrange(self.isotopeNumbers[j]):
+                for k in range(self.isotopeNumbers[j]):
                     newl.append(i)
                     i += 1
                 offsets.append(tuple(newl))
@@ -289,10 +284,10 @@ def np_probs(self):
 
     def __iter__(self):
         if hasattr(self, "confs") and self.confs is not None:
-            for i in xrange(self.size):
+            for i in range(self.size):
                 yield(self.masses[i], self.probs[i], self.confs[i])
         else:
-            for i in xrange(self.size):
+            for i in range(self.size):
                 yield (self.masses[i], self.probs[i])
 
     def __getitem__(self, idx):

src/IsoSpecPy/IsoSpecPyOld.py

@@ -9,7 +9,7 @@
 #
 #   IsoSpec is distributed in the hope that it will be useful,
 #   but WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 #
 #   You should have received a copy of the Simplified BSD Licence
 #   along with IsoSpec.  If not, see <https://opensource.org/licenses/BSD-2-Clause>.
@@ -26,10 +26,6 @@
 The current API is implemented in __init__.py, use that instead
 '''
 
-try:
-    xrange
-except NameError:
-    xrange = range
 
 import re
 from .IsoSpecPy import IsoTotalProb, IsoThreshold
@@ -80,7 +76,7 @@ def __init__(
         except KeyError:
             raise Exception("Invalid ISO method")
 
-        # Reference to iso needs to be held in this object: it will deallocate masses/lprobs/etc arrays on C++ side if we 
+        # Reference to iso needs to be held in this object: it will deallocate masses/lprobs/etc arrays on C++ side if we
         # allow GC to collect it prematurely
         self.iso = algo(_stopCondition)
 
@@ -136,7 +132,7 @@ def getConfs(self):
         masses  = list(masses)
         logProbs= list(logProbs)
         confs = []
-        for i in xrange(rows_no):
+        for i in range(rows_no):
             confs.append([x for sublist in isoCounts[i] for x in sublist])
         return masses, logProbs, confs
 
@@ -157,7 +153,7 @@ def getConfsNumpy(self):
     def splitConf(self, l, offset = 0):
         conf = []
         idx = self.allIsotopeNumber * offset
-        for i in xrange(self.dimNumber):
+        for i in range(self.dimNumber):
             conf.append(tuple(l[idx:idx+self._isotopeNumbers[i]]))
             idx += self._isotopeNumbers[i]
         return tuple(conf)
@@ -169,7 +165,7 @@ def printConfs(self):
         masses, logProbs, isoCounts = self.getConfsRaw()
         confs = []
         step = sum(self._isotopeNumbers)
-        for i in xrange(len(masses)):
+        for i in range(len(masses)):
             confs.append((masses[i], logProbs[i], self.splitConf(isoCounts, i)))
 
         for conf in confs:
@@ -184,7 +180,7 @@ def __init__(self, iso, bin_w):
         self.bin_w = bin_w
         masses, logProbs, _isoCounts = iso.getConfsRaw()
         dd = defaultdict(Summator)
-        for i in xrange(len(masses)):
+        for i in range(len(masses)):
             dd[float(int(masses[i]/bin_w))*bin_w].add(math.exp(logProbs[i]))
         for key, val in dd.items():
             self[key] = val.get()

src/IsoSpecPy/PeriodicTbl.py

@@ -1,10 +1,6 @@
 from .isoFFI import isoFFI
 from collections import defaultdict
 
-try:
-    xrange
-except NameError:
-    xrange = range
 
 number_of_isotopic_entries = isoFFI.clib.NUMBER_OF_ISOTOPIC_ENTRIES
 
@@ -13,7 +9,7 @@
 symbol_to_probs  = defaultdict(tuple)
 symbol_to_atomic_number = {}
 
-for i in xrange(number_of_isotopic_entries):
+for i in range(number_of_isotopic_entries):
     symbol = isoFFI.ffi.string(isoFFI.clib.elem_table_symbol[i]).decode("ascii")
     symbol_to_masses[symbol] += (isoFFI.clib.elem_table_mass[i],)
     symbol_to_massNo[symbol] += (isoFFI.clib.elem_table_massNo[i],)

tests/cppyy/cpt.py

@@ -5,4 +5,4 @@
 i = cppyy.gbl.IsoSpec.Iso("C100H100")
 iso = cppyy.gbl.IsoSpec.IsoThresholdGenerator(cppyy.gbl.std.move(i), 0.01)
 while iso.advanceToNextConfiguration():
-    print iso.prob(), iso.mass()
+    print(iso.prob(), iso.mass())

tests/cppyy/overhead-cppyy.py

@@ -10,7 +10,7 @@
 
 
 t = 0.0
-for x in tqdm(xrange(1000000)):
+for x in tqdm(range(1000000)):
     i = cppyy.gbl.IsoSpec.Iso("C100H100N100O100")
     t += i.getTheoreticalAverageMass()
-print t
+print(t)

tests/cppyy/overhead.py

@@ -2,7 +2,7 @@
 from tqdm import tqdm
 
 t = 0.0
-for x in tqdm(xrange(100000)):
+for x in tqdm(range(100000)):
     i = IsoSpecPy.Iso("C100H100N100O100")
     t += i.getTheoreticalAverageMass()
-print t
+print(t)