Python 3 migration of PyHEADTAIL v1.13.5

PyHEADTAIL/__init__.py

@@ -22,7 +22,7 @@
     from ._version import __version__
     dirty = False
 
-print ('PyHEADTAIL v' + __version__)
+print(('PyHEADTAIL v' + __version__))
 if dirty:
     print ('(dirty git work tree)')
 print ('\n')

PyHEADTAIL/aperture/aperture.py

@@ -10,7 +10,7 @@
          Michael Schenk
 '''
 
-from __future__ import division
+
 
 import numpy as np
 from abc import ABCMeta, abstractmethod
@@ -23,15 +23,13 @@ def make_int32(array):
     return array.astype(np.int32)
 
 
-class Aperture(Element):
+class Aperture(Element, metaclass=ABCMeta):
     '''Abstract base class for Aperture elements. An aperture is
     generally defined as a condition on the phase space coordinates.
     Particles not fulfilling this condition are tagged as lost and
     are removed from the beam directly after.
     '''
 
-    __metaclass__ = ABCMeta
-
     @clean_slices
     def track(self, beam):
         '''Tag particles not passing through the aperture as lost. If

PyHEADTAIL/cobra_functions/curve_tools.py

@@ -1,4 +1,4 @@
-from __future__ import division
+
 
 import numpy as np
 from scipy.optimize import brentq
@@ -20,4 +20,4 @@ def extrema(x, y=None):
     zix = np.where(np.abs(np.diff(np.sign(np.diff(x)))) == 2)[0]
     return zix
     if not y:
-        print zix
+        print(zix)

PyHEADTAIL/feedback/transverse_damper.py

@@ -4,7 +4,7 @@
 @copyright CERN
 '''
 
-from __future__ import division
+
 
 import numpy as np
 from scipy.special import k0

PyHEADTAIL/feedback/widebandfeedback.py

@@ -4,7 +4,7 @@
 @copyright CERN
 '''
 
-from __future__ import division
+
 
 import numpy as np
 from scipy.special import k0

PyHEADTAIL/field_maps/Transverse_Efield_map.py

@@ -36,7 +36,7 @@ def track(self, beam):
 
         slices = beam.get_slices(self.slicer)
 
-        for sid in xrange(slices.n_slices-1, -1, -1):
+        for sid in range(slices.n_slices-1, -1, -1):
 
             # select particles in the slice
             pid = slices.particle_indices_of_slice(sid)

PyHEADTAIL/field_maps/field_map.py

@@ -15,7 +15,7 @@
 @date:    13.06.2017
 '''
 
-from __future__ import division, print_function
+
 
 from scipy.constants import c
 
@@ -82,7 +82,7 @@ def __init__(self, length, mesh, fields, wrt_beam_centroid=False,
             poissonsolver=None,
             gradient=lambda *args, **kwargs: None,
             mesh=mesh)
-        self.fields = map(pm.ensure_same_device, fields)
+        self.fields = list(map(pm.ensure_same_device, fields))
         self.wrt_beam_centroid = wrt_beam_centroid
 
     def track(self, beam):
@@ -94,7 +94,7 @@ def track(self, beam):
                      beam.y - my,
                      beam.z - mz] # zip will cut to #fields
 
-        mesh_fields_and_mp_coords = zip(self.fields, mp_coords)
+        mesh_fields_and_mp_coords = list(zip(self.fields, mp_coords))
 
         # electric fields at each particle position in lab frame [V/m]
         part_fields = self.pypic.field_to_particles(*mesh_fields_and_mp_coords)
@@ -149,7 +149,7 @@ def __init__(self, slicer, *args, **kwargs):
         # require 2D!
         assert self.pypic.mesh.dimension == 2, \
             'mesh needs to be two-dimensional!'
-        assert all(map(lambda f: f.ndim == 2, self.fields)), \
+        assert all([f.ndim == 2 for f in self.fields]), \
             'transverse field components need to be two-dimensional arrays!'
         #
 
@@ -167,7 +167,7 @@ def track(self, beam):
         mp_coords = [beam.x - mx,
                      beam.y - my,
                      beam.z] # zip will cut to #fields
-        mesh_fields_and_mp_coords = zip(self.fields, mp_coords)
+        mesh_fields_and_mp_coords = list(zip(self.fields, mp_coords))
 
         # electric fields at each particle position in lab frame [V/m]
         part_fields = self.pypic.field_to_particles(*mesh_fields_and_mp_coords)

PyHEADTAIL/general/decorators.py

@@ -26,7 +26,7 @@ def deprecated_wrapper(*args, **kwargs):
                           'PyHEADTAIL release!'.format(name),
                           category=DeprecationWarning, stacklevel=2)
             warnings.simplefilter('default', DeprecationWarning)
-            print message
+            print(message)
             return func(*args, **kwargs)
         return deprecated_wrapper
     return deprecated_decorator
@@ -41,7 +41,7 @@ def memoize(function):
     @wraps(function)
     def evaluate(*args):
         signature = (args)
-        if not store.has_key(signature):
+        if signature not in store:
             store[signature] = function(*args)
         return store[signature]
     return evaluate

PyHEADTAIL/general/element.py

@@ -71,12 +71,11 @@ def warns(self, output):
         self._warningprinter.prints("*** PyHEADTAIL WARNING! " + output)
 
 
-class Element(Printing):
+class Element(Printing, metaclass=ABCMeta):
     '''
     Abstract element as part of the tracking layout. Guarantees
     to fulfil its tracking contract via the method track(beam).
     '''
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def track(self, beam):

PyHEADTAIL/general/pmath.py

@@ -331,8 +331,8 @@ def update_active_dict(new_dict):
     if not hasattr(update_active_dict, 'active_dict'):
         update_active_dict.active_dict = new_dict
     # delete all old implementations/references from globals()
-    for key in globals().keys():
-        if key in update_active_dict.active_dict.keys():
+    for key in list(globals().keys()):
+        if key in list(update_active_dict.active_dict.keys()):
             del globals()[key]
     # add the new active dict to the globals()
     globals().update(new_dict)

PyHEADTAIL/general/printers.py

@@ -9,7 +9,7 @@
 from abc import ABCMeta, abstractmethod
 
 
-class Printer(object):
+class Printer(object, metaclass=ABCMeta):
     '''
     A generic printer knows where to redirect text for print.
     Use Printer.prints(output) to print the output instead of
@@ -22,7 +22,6 @@ class Printer(object):
     a file or use different streams for errors, warnings and content
     related output etc.
     '''
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def prints(self, output):

PyHEADTAIL/gpu/gpu_utils.py

@@ -38,10 +38,10 @@
     atexit.register(skcuda.misc.shutdown)
 
     n_streams = 4
-    streams = [drv.Stream() for i in xrange(n_streams)]
+    streams = [drv.Stream() for i in range(n_streams)]
     stream_pool = cycle(streams)
 
-    stream_emittance = [drv.Stream() for i in xrange(6)]
+    stream_emittance = [drv.Stream() for i in range(6)]
 
 
     def dummy_1(gpuarr, stream=None):

PyHEADTAIL/gpu/gpu_wrap.py

@@ -5,10 +5,10 @@
 Use in dispatch of general/pmath
 All functions assume GPU arrays as arguments!
 '''
-from __future__ import division
+
 import numpy as np
 import os
-import gpu_utils
+from . import gpu_utils
 import math
 from functools import wraps
 try:
@@ -226,7 +226,7 @@ def sign(array, out=None, stream=None):
                   'else notclose[i] = 0;',
         name='allclose_kernel'
     )
-    np_allclose_defaults = np.allclose.func_defaults # (rtol, atol, equal_nan)
+    np_allclose_defaults = np.allclose.__defaults__ # (rtol, atol, equal_nan)
     @wraps(np.allclose)
     def allclose(a, b, rtol=np_allclose_defaults[0],
                  atol=np_allclose_defaults[1], out=None, stream=None):
@@ -565,9 +565,9 @@ def argsort(to_sort):
     elif dtype.itemsize == 4 and dtype.kind is 'i':
         thrust.get_sort_perm_int(to_sort.copy(), permutation)
     else:
-        print to_sort.dtype
-        print to_sort.dtype.itemsize
-        print to_sort.dtype.kind
+        print(to_sort.dtype)
+        print(to_sort.dtype.itemsize)
+        print(to_sort.dtype.kind)
         raise TypeError('Currently only float64 and int32 types can be sorted')
     return permutation
 
@@ -603,9 +603,9 @@ def apply_permutation(array, permutation):
     elif dtype.itemsize == 4 and dtype.kind is 'i':
         thrust.apply_sort_perm_int(array, tmp, permutation)
     else:
-        print array.dtype
-        print array.dtype.itemsize
-        print array.dtype.kind
+        print(array.dtype)
+        print(array.dtype.itemsize)
+        print(array.dtype.kind)
         raise TypeError('Currently only float64 and int32 types can be sorted')
     return tmp
 

PyHEADTAIL/gpu/particles.py

@@ -1,6 +1,6 @@
 # default classes imports from modules as assigned in gpu/__init__.py
 import numpy as np
-import thrust_interface as thrust
+from . import thrust_interface as thrust
 from pycuda import gpuarray
 
 from PyHEADTAIL.gpu.oldinit import def_particles

PyHEADTAIL/gpu/slicing.py

@@ -2,7 +2,7 @@
 @authors: Adrian Oeftiger
 @date:    30/07/2015
 '''
-from __future__ import division
+
 
 import os
 where = os.path.dirname(os.path.abspath(__file__)) + '/'

PyHEADTAIL/gpu/wrapper.py

@@ -1,4 +1,4 @@
-from __future__ import division
+
 
 from pycuda.elementwise import ElementwiseKernel
 from PyHEADTAIL.trackers import wrapper as def_wrapper

PyHEADTAIL/impedances/wake_kicks.py

@@ -7,7 +7,7 @@
 @copyright CERN
 """
 
-from __future__ import division
+
 
 import numpy as np
 from scipy.constants import c
@@ -16,7 +16,7 @@
 from PyHEADTAIL.general import pmath as pm
 from PyHEADTAIL.general.element import Printing
 
-class WakeKick(Printing):
+class WakeKick(Printing, metaclass=ABCMeta):
     """Abstract base class for wake kick classes, like e.g. the
     DipoleWakeKickX.
     Provides the basic and universal methods to calculate the strength
@@ -30,8 +30,6 @@ class WakeKick(Printing):
     the WakeKick class.
     """
 
-    __metaclass__ = ABCMeta
-
     def __init__(self, wake_function, slicer, n_turns_wake,
                  *args, **kwargs):
         """Universal constructor for WakeKick objects. The slicer_mode

PyHEADTAIL/impedances/wakes.py

@@ -20,7 +20,7 @@
 @copyright CERN
 """
 
-from __future__ import division
+
 
 import numpy as np
 from collections import deque
@@ -69,7 +69,7 @@ def check_wake_sampling(bunch, slicer, wakes, beta=1, wake_column=None, bins=Fal
         lgd += ['Bin edges']
     ax2.legend(lgd)
 
-    print '\n--> Resulting number of slices: {:g}'.format(len(ss))
+    print('\n--> Resulting number of slices: {:g}'.format(len(ss)))
 
     return ax1
 
@@ -132,7 +132,7 @@ def track(self, bunch):
         WakeKick instances. """
 
         # Update ages of stored SliceSet instances.
-        for i in xrange(len(self.slice_set_age_deque)):
+        for i in range(len(self.slice_set_age_deque)):
             self.slice_set_age_deque[i] += (
                 bunch.circumference / (bunch.beta * c))
 
@@ -147,10 +147,9 @@ def track(self, bunch):
 
 ''' WakeSource classes. '''
 
-class WakeSource(Printing):
+class WakeSource(Printing, metaclass=ABCMeta):
     """ Abstract base class for wake sources, such as WakeTable,
     Resonator or ResistiveWall. """
-    __metaclass__ = ABCMeta
 
     @abstractmethod
     def get_wake_kicks(self, slicer_mode):
@@ -287,7 +286,7 @@ def get_wake_kicks(self, slicer):
     def _is_provided(self, wake_component):
         """ Check whether wake_component is a valid name and available
         in wake table data. Return 'True' if yes and 'False' if no. """
-        if wake_component in self.wake_table.keys():
+        if wake_component in list(self.wake_table.keys()):
             return True
         else:
             # self.warns(wake_component + ' \n' +

PyHEADTAIL/machines/synchrotron.py

@@ -1,4 +1,4 @@
-from __future__ import division
+
 
 import numpy as np
 from scipy.constants import c
@@ -268,7 +268,7 @@ def _construct_transverse_map(
         self.transverse_map.n_segments = len(s)-1
 
         if name is None:
-            self.transverse_map.name = ['P_%d' % ip for ip in xrange(len(s)-1)]
+            self.transverse_map.name = ['P_%d' % ip for ip in range(len(s)-1)]
             self.transverse_map.name.append('end_ring')
         else:
             self.transverse_map.name = name

PyHEADTAIL/monitors/monitors.py

@@ -6,7 +6,7 @@
 @copyright CERN
 """
 
-from __future__ import division
+
 
 import h5py as hp
 import numpy as np
@@ -22,13 +22,11 @@
 # from .. import cobra_functions.stats.calc_cell_stats as calc_cell_stats
 
 
-class Monitor(Printing):
+class Monitor(Printing, metaclass=ABCMeta):
     """ Abstract base class for monitors. A monitor can request
     statistics data such as mean value and standard deviation and store
     the results in an HDF5 file. """
 
-    __metaclass__ = ABCMeta
-
     @abstractmethod
     def dump(bunch):
         """ Write particle data given by bunch (instance of Particles
@@ -445,7 +443,7 @@ def _write_data_to_file(self, bunch, arrays_dict):
         h5file = hp.File(self.filename + '.h5part', 'a')
         h5group = h5file.create_group('Step#' + str(self.i_steps))
         dims = (bunch.macroparticlenumber // self.stride,)
-        dims = bunch.get_coords_n_momenta_dict().values()[0][::self.stride].shape # more robust implementation
+        dims = list(bunch.get_coords_n_momenta_dict().values())[0][::self.stride].shape # more robust implementation
 
         # resorting_indices = np.argsort(bunch.id)[::self.stride]
         all_quantities = {}
@@ -462,7 +460,7 @@ def _write_data_to_file(self, bunch, arrays_dict):
         if arrays_dict is not None:
             all_quantities.update(arrays_dict)
 
-        for quant in all_quantities.keys():
+        for quant in list(all_quantities.keys()):
             quant_values = all_quantities[quant]
             h5group.create_dataset(quant, shape=dims, compression='gzip',
                 compression_opts=9, dtype=quant_values.dtype)