Merge pull request #112 from PyCOMPLETE/release/v1.14.0

Release/v1.14.0

PyHEADTAIL/__init__.py

@@ -22,13 +22,11 @@
     from ._version import __version__
     dirty = False
 
-print ('PyHEADTAIL v' + __version__)
+print(('PyHEADTAIL v' + __version__))
 if dirty:
     print ('(dirty git work tree)')
 print ('\n')
 
-from .general.element import Element, Printing
-from .general import utils
 # print '                                                                                                                             '
 # print '                                                                ;Cfttttt11111111tttt1f0f.                                    '
 # print '                                                                ,GttttfG0GGG00000GGG0G0G0G0G0G0Ct1t1fG:                      '

PyHEADTAIL/_version.py

@@ -1 +1 @@
-__version__ = '1.13.5'
+__version__ = '1.14.0'

PyHEADTAIL/aperture/__init__.py

@@ -1,4 +1 @@
-from .. import Element
-from ..particles.slicing import clean_slices
-from .. import __version__
 

PyHEADTAIL/aperture/aperture.py

@@ -1,4 +1,3 @@
-from __future__ import division
 '''
 Aperture module to manage particle losses. An aperture is
 defined as a condition on the phase space coordinates. Particles
@@ -11,26 +10,26 @@
          Michael Schenk
 '''
 
-from . import Element, clean_slices
 
-from abc import ABCMeta, abstractmethod
 
-from ..general import pmath as pm
 import numpy as np
+from abc import ABCMeta, abstractmethod
+
+from PyHEADTAIL.general.element import Element, Printing
+from PyHEADTAIL.general import pmath as pm
+from PyHEADTAIL.particles.slicing import clean_slices
 
 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/aperture/aperture_cython.pyx

@@ -17,7 +17,7 @@ cimport cython
 import numpy as np
 cimport numpy as np
 
-import aperture
+import PyHEADTAIL.aperture.aperture as aperture
 
 class Aperture(aperture.Aperture):
     '''Pendant to aperture.Aperture with the relocate algorithm

PyHEADTAIL/cobra_functions/__init__.py

@@ -1 +0,0 @@
-from .. import __version__

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/cobra_functions/pdf_integrators_2d.py

@@ -3,9 +3,9 @@
 @date 21.06.2017
 @brief 2D distribution integration methods for y(x) parametrised domains
 '''
-from scipy.integrate import quad, dblquad, cumtrapz, romb
 
 import numpy as np
+from scipy.integrate import quad, dblquad, cumtrapz, romb
 
 
 def quad2d(f, ylimits, xmin, xmax):

PyHEADTAIL/cobra_functions/stats.pyx

@@ -5,6 +5,7 @@
        of bunch and slice_set data.
 @copyright CERN
 """
+
 import numpy as np
 cimport numpy as np
 cimport libc.math as cmath

PyHEADTAIL/feedback/__init__.py

@@ -1,2 +0,0 @@
-from .. import __version__
-from .. import Element

PyHEADTAIL/feedback/transverse_damper.py

@@ -3,14 +3,14 @@
 @date 20/06/2014
 @copyright CERN
 '''
-from __future__ import division
+
 
 
 import numpy as np
 from scipy.special import k0
 from scipy.constants import c, e
 
-from . import Element
+from PyHEADTAIL.general.element import Element
 
 class TransverseDamper(Element):
 

PyHEADTAIL/feedback/widebandfeedback.py

@@ -3,7 +3,7 @@
 @date 20/06/2014
 @copyright CERN
 '''
-from __future__ import division
+
 
 
 import numpy as np

PyHEADTAIL/field_maps/Transverse_Efield_map.py

@@ -1,16 +1,16 @@
 import numpy as np
 from scipy.constants import c
 
+from PyHEADTAIL.general.element import Element
 from PyHEADTAIL.particles.slicing import UniformBinSlicer
 from PyPIC.PyPIC_Scatter_Gather import PyPIC_Scatter_Gather
 
-from . import Element
 
 class Transverse_Efield_map(Element):
     def __init__(self, xg, yg, Ex, Ey, L_interaction, slicer,
-        	flag_clean_slices=False, wrt_slice_centroid=False,
-        	x_beam_offset=0., y_beam_offset=0., verbose=False,
-            *args, **kwargs):
+                 flag_clean_slices=False, wrt_slice_centroid=False,
+                 x_beam_offset=0., y_beam_offset=0., verbose=False,
+                 *args, **kwargs):
 
         self.slicer = slicer
         self.L_interaction = L_interaction
@@ -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/__init__.py

@@ -1 +0,0 @@
-from .. import Element

PyHEADTAIL/field_maps/field_map.py

@@ -15,14 +15,13 @@
 @date:    13.06.2017
 '''
 
-from __future__ import division, print_function
 
-from scipy.constants import c
 
-from . import Element
+from scipy.constants import c
 
-from ..general import pmath as pm
-from ..gpu.pypic import make_PyPIC
+from PyHEADTAIL.general.element import Element
+from PyHEADTAIL.general import pmath as pm
+from PyHEADTAIL.gpu.pypic import make_PyPIC
 
 class FieldMap(Element):
     '''This static field in the lab frame applies kicks to the beam
@@ -83,7 +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):
@@ -95,7 +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)
@@ -150,7 +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!'
         #
 
@@ -168,7 +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/__init__.py

@@ -1 +0,0 @@
-from .. import __version__

PyHEADTAIL/general/contextmanager.py

@@ -3,18 +3,12 @@
 @author Stefan Hegglin
 @data 30.09.2015
 '''
+
 import numpy as np
 
-class UnknownContextManagerError(Exception):
-    '''Raise if context manager is not found, e.g. cannot determine
-    whether on CPU or on GPU.
-    '''
-    def __init__(self, message='Failed to determine current context, e.g. '
-                               'whether pmath.device is "CPU" or "GPU".'):
-        self.message = message
+import PyHEADTAIL.general.pmath as pm
+from PyHEADTAIL.gpu import gpu_utils
 
-import pmath as pm
-from ..gpu import gpu_utils
 try:
     import pycuda.gpuarray as gpuarray
     import pycuda
@@ -25,6 +19,7 @@ def __init__(self, message='Failed to determine current context, e.g. '
     # print ('pycuda not found, GPU context unavailable')
     has_pycuda = False
 
+
 if has_pycuda:
     def create_kernel(operator):
         '''Return a elementwisekernel with the operator being one of

PyHEADTAIL/general/decorators.py

@@ -7,7 +7,8 @@
 
 import warnings
 from functools import wraps
-from ..gpu import gpu_utils
+
+from PyHEADTAIL.gpu import gpu_utils
 
 
 def deprecated(message):
@@ -25,7 +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
@@ -40,7 +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

@@ -7,9 +7,11 @@
 Can be used for implementing general features that every derived element
 in PyHEADTAIL should have.
 '''
-from .printers import ConsolePrinter
+
 from abc import ABCMeta, abstractmethod
 
+from PyHEADTAIL.general.printers import ConsolePrinter
+
 
 class Printing(object):
     '''Provides prints(output) method in order to communicate any output
@@ -24,6 +26,9 @@ class Printing(object):
     in order to obtain full flexibility over output channels.
     '''
 
+    def __init__(self, *args, **kwargs):
+        pass
+
     def __new__(cls, *args, **kwargs):
         '''
         Factory method makes sure that inheriting elements always
@@ -66,12 +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

@@ -4,39 +4,53 @@
 @author Stefan Hegglin
 @date 05.10.2015
 '''
+
 import numpy as np
-from ..cobra_functions import stats as cp
+from functools import wraps
+from scipy.special import erfc as _erfc
+from scipy.special import wofz as _scipy_wofz
+
+from PyHEADTAIL.cobra_functions import stats as cp
+
 try:
     import pycuda.cumath
     import pycuda.gpuarray
     import pycuda.tools
-    from ..gpu import gpu_utils
-    from ..gpu import gpu_wrap
+
+    from PyHEADTAIL.gpu import gpu_utils
+    from PyHEADTAIL.gpu import gpu_wrap
     has_pycuda = gpu_wrap.has_pycuda
 except (ImportError, OSError):
     # print ('No Pycuda in pmath.py import statement found')
     has_pycuda = False
+
 try:
     import skcuda.misc
 except ImportError:
     # print ('Skcuda not found. (Scikit-cuda)')
     pass
 
-from functools import wraps
-
-from contextmanager import UnknownContextManagerError
-
 # FADDEEVA error function (wofz) business (used a.o. in spacecharge module)
 try:
-    from errfff import errf as _errf_f
+    from PyHEADTAIL.general.errfff import errf as _errf_f
     _errf = np.vectorize(_errf_f)
 except ImportError:
     _errf = None
-from scipy.special import erfc as _erfc
-from scipy.special import wofz as _scipy_wofz
+
+
+class UnknownContextManagerError(Exception):
+    '''Raise if context manager is not found, e.g. cannot determine
+    whether on CPU or on GPU.
+    '''
+    def __init__(self, message='Failed to determine current context, e.g. '
+                               'whether pmath.device is "CPU" or "GPU".'):
+        self.message = message
+
+
 def _wofz(x, y):
     res = _scipy_wofz(x + 1j*y)
     return res.real, res.imag
+
 def _errfadd(z):
     return np.exp(-z**2) * _erfc(z * -1j)
 
@@ -317,8 +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)