Remove residual Python2-specific code

CMakeLists.txt

@@ -235,7 +235,7 @@ if(WITH_CUDA)
   endif()
 endif(WITH_CUDA)
 
-find_package(PythonInterp 3.2 REQUIRED)
+find_package(PythonInterp 3.3 REQUIRED)
 
 if(WITH_PYTHON)
   find_package(Cython 0.23 REQUIRED)
@@ -253,25 +253,15 @@ if(WITH_PYTHON)
       OUTPUT_VARIABLE PYTHON_INSTDIR
       OUTPUT_STRIP_TRAILING_WHITESPACE)
   endif(NOT PYTHON_INSTDIR)
-  if(PYTHON_VERSION_MAJOR EQUAL 2)
-    set(
-      CYTHON_FLAGS "-2"
-      CACHE STRING "Flags used by the Cython compiler during all build types.")
-  else()
-    set(
-      CYTHON_FLAGS "-3"
+
+  set(CYTHON_FLAGS "-3"
       CACHE STRING "Flags used by the Cython compiler during all build types.")
-  endif()
 
   if(WARNINGS_ARE_ERRORS)
     set(CYTHON_FLAGS "--warning-errors;${CYTHON_FLAGS}")
   endif()
 
-  if(PYTHON_VERSION_MAJOR EQUAL 2)
-    find_program(IPYTHON_EXECUTABLE NAMES ipython2 ipython jupyter)
-  else()
-    find_program(IPYTHON_EXECUTABLE NAMES ipython3 ipython jupyter)
-  endif()
+  find_program(IPYTHON_EXECUTABLE NAMES jupyter ipython3 ipython)
 endif(WITH_PYTHON)
 
 
@@ -280,7 +270,7 @@ if(FFTW3_FOUND)
   set(FFTW 3)
 endif(FFTW3_FOUND)
 
-# If we build either interface turn on script interface
+# If we build Python bindings, turn on script interface
 if(WITH_PYTHON)
   set(WITH_SCRIPT_INTERFACE ON)
 endif()

maintainer/CI/build_cmake.sh

@@ -164,8 +164,6 @@ pep8_command () {
         pep8 "$@"
     elif hash pycodestyle 2> /dev/null; then
         pycodestyle "$@"
-    elif hash pycodestyle-2 2> /dev/null; then
-        pycodestyle-2 "$@"
     elif hash pycodestyle-3 2> /dev/null; then
         pycodestyle-3 "$@"
     else
@@ -192,8 +190,6 @@ pylint_command () {
         pylint "$@"
     elif hash pylint3 2> /dev/null; then
         pylint3 "$@"
-    elif hash pylint-2 2> /dev/null; then
-        pylint-2 "$@"
     elif hash pylint-3 2> /dev/null; then
         pylint-3 "$@"
     else
@@ -206,7 +202,6 @@ if [ $(pylint_command --version | grep -o 'pylint.*[0-9]\.[0-9]\.[0-9]' | awk '{
 else
     score_option=''
 fi
-pylint_command ${score_option} --reports=no --disable=all --enable=C1001 $(find . -name '*.py*') || { echo -e "\nOld-style classes found.\nPlease convert to new-style:\nclass C: => class C(object):\n" && exit 1; }
 
 if [ ${insource} = false ]; then
     if [ ! -d "${builddir}" ]; then

src/config/defines.py

@@ -19,7 +19,7 @@
 from sys import argv
 
 
-class Defines(object):
+class Defines:
 
     def __init__(self, compiler, flags=[]):
         self._compiler = compiler

src/config/featuredefs.py

@@ -24,7 +24,7 @@
 import re
 
 
-class SyntaxError(object):
+class SyntaxError:
 
     def __init__(self, message, instead):
         self.message = message
@@ -45,7 +45,7 @@ def toCPPExpr(expr):
     return expr
 
 
-class defs(object):
+class defs:
 
     def __init__(self, filename):
         # complete set of all defined features

src/python/espressomd/MDA_ESP/__init__.py

@@ -71,7 +71,7 @@
 )
 
 
-class Stream(object):
+class Stream:
 
     """
     Create an object that provides a MDAnalysis topology and a coordinate reader

src/python/espressomd/__init__.py

@@ -31,7 +31,7 @@ class FeaturesError(Exception):
 
     def __init__(self, missing_features_list):
         message = "Missing features " + ", ".join(missing_features_list)
-        super(FeaturesError, self).__init__(message)
+        super().__init__(message)
 
 
 def has_features(*args):

src/python/espressomd/actors.pyx

@@ -2,7 +2,7 @@ include "myconfig.pxi"
 from .highlander import ThereCanOnlyBeOne
 from .utils import handle_errors
 
-cdef class Actor(object):
+cdef class Actor:
 
     """
     Abstract base class for interactions affecting particles in the system,
@@ -169,7 +169,7 @@ cdef class Actor(object):
             "Subclasses of %s must define the _deactivate_method() method." % self._get_interaction_type())
 
 
-class Actors(object):
+class Actors:
 
     """
     Container for :class:`Actor` objects.

src/python/espressomd/analyze.pyx

@@ -40,7 +40,7 @@ from .system import System
 from espressomd.utils import is_valid_type
 
 
-class Analysis(object):
+class Analysis:
 
     def __init__(self, system):
         if not isinstance(system, System):

src/python/espressomd/cellsystem.pyx

@@ -24,7 +24,7 @@ import numpy as np
 from espressomd.utils cimport handle_errors
 from espressomd.utils import is_valid_type
 
-cdef class CellSystem(object):
+cdef class CellSystem:
     def set_domain_decomposition(
         self,
         use_verlet_lists=True,

src/python/espressomd/checkpointing.py

@@ -31,7 +31,7 @@
 
 
 # Convenient Checkpointing for ESPResSo
-class Checkpoint(object):
+class Checkpoint:
 
     """Checkpoint handling (reading and writing).
 

src/python/espressomd/cluster_analysis.py

@@ -29,7 +29,7 @@ class Cluster(ScriptInterfaceHelper):
         Returns list of particle ids in the cluster
 
     particles():
-        Returns an instance of ParticleSlice containing the paritlces in the cluster
+        Returns an instance of ParticleSlice containing the particles in the cluster
 
     size():
         Returns the number of particles in the cluster
@@ -42,9 +42,9 @@ class Cluster(ScriptInterfaceHelper):
 
     fractal_dimension(dr=None):
         estimates the cluster's fractal dimension by fitting the number of particles
-        :math:`n` in spheres of growing radius around the cetner of mass
+        :math:`n` in spheres of growing radius around the center of mass
         to :math:`c*r_g^d`, where :math:`r_g` is the radius of gyration of the particles
-        witin the sphere, and :math:`d` is the fractal dimensoin.
+        within the sphere, and :math:`d` is the fractal dimension.
         `dr`: Minimum increment for the radius of the spheres.
         Return value: (fractal_dimension, mean_square_residual)
     """
@@ -61,7 +61,7 @@ def particles(self):
 @script_interface_register
 class ClusterStructure(ScriptInterfaceHelper):
 
-    """Cluster structure of a simulation system, and access to cluster anaylsis
+    """Cluster structure of a simulation system, and access to cluster analysis
 
     Attributes
     ----------
@@ -70,17 +70,19 @@ class ClusterStructure(ScriptInterfaceHelper):
 
     clusters: behaves like a read-only dictionary
         Access to individual clusters in the cluster structure either via
-        cluster[i], wher i is a (non-consecutive) integer cluster id
-        or via iteration:
-        for pair in clusters:
+        cluster[i], where i is a (non-consecutive) integer cluster id
+        or via iteration::
+
+            for pair in clusters:
+
         where pair contains the numeric id and the corresponding cluster object.
 
     """
     _so_name = "ClusterAnalysis::ClusterStructure"
     _so_creation_policy = "LOCAL"
 
     def __init__(self, *args, **kwargs):
-        super(type(self), self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._clusters = Clusters(self)
 
     def run_for_all_pairs(self):
@@ -92,7 +94,7 @@ def run_for_all_pairs(self):
 
     def run_for_bonded_particles(self):
         """
-        Runts the cluster analysis, considering only pairs of particles connected ba a pair-bond.
+        Runs the cluster analysis, considering only pairs of particles connected by a pair-bond.
 
         """
         return self.call_method("run_for_bonded_particles")
@@ -126,15 +128,15 @@ def clusters(self):
         return self._clusters
 
 
-class Clusters(object):
+class Clusters:
 
     """Access to the clusters in the cluster structure.
 
        Access is as follows:
 
        * Number of clusters: len(clusters)
        * Access a cluster via its id: clusters[id]
-       * Iterate over clusters:::
+       * Iterate over clusters::
 
             for c in clusters:
 

src/python/espressomd/collision_detection.pyx

@@ -34,7 +34,7 @@ class CollisionDetection(ScriptInterfaceHelper):
         # If no mode is specified at construction, use off.
         if "mode" not in kwargs:
             kwargs["mode"] = "off"
-        super(type(self), self).__init__()
+        super().__init__()
         self.set_params(**kwargs)
 
     def validate(self):
@@ -48,7 +48,7 @@ class CollisionDetection(ScriptInterfaceHelper):
     # Do not allow setting of individual attributes
     def __setattr__(self, *args, **kwargs):
         raise Exception(
-            "Please et all parameters at once via collision_detection.set_params()")
+            "Please set all parameters at once via collision_detection.set_params()")
 
     # Override to call validate after parameter update
     def set_params(self, **kwargs):
@@ -76,13 +76,13 @@ class CollisionDetection(ScriptInterfaceHelper):
                Particle type of the virtual sites being created on collision (virtual sites based modes)
 
         part_type_to_be_glued : :obj:`int`
-               particle type for "glue_to_surface|" mode. See user guide.
+               particle type for "glue_to_surface" mode. See user guide.
 
         part_type_to_attach_vs_to : :obj:`int`
-               particle type for "glue_to_surface|" mode. See user guide.
+               particle type for "glue_to_surface" mode. See user guide.
 
         part_type_after_glueing : :obj:`int`
-               particle type for "glue_to_surface|" mode. See user guide.
+               particle type for "glue_to_surface" mode. See user guide.
 
         distance_glued_particle_to_vs : :obj:`float`
                Distance for "glue_to_surface" mode. See user guide.
@@ -103,7 +103,7 @@ class CollisionDetection(ScriptInterfaceHelper):
         # Completeness of parameter set
         if not (set(kwargs.keys()) == set(self._params_for_mode(kwargs["mode"]))):
             raise Exception("Parameter set does not match mode. ", kwargs[
-                            "mode"], "requries ", self._params_for_mode(kwargs["mode"]))
+                            "mode"], "requires ", self._params_for_mode(kwargs["mode"]))
 
         # Mode
         kwargs["mode"] = self._int_mode[kwargs["mode"]]
@@ -113,21 +113,21 @@ class CollisionDetection(ScriptInterfaceHelper):
             if name in kwargs:
                 if isinstance(kwargs[name], BondedInteraction):
                     kwargs[name] = kwargs[name]._bond_id
-        super(type(self), self).set_params(**kwargs)
+        super().set_params(**kwargs)
         self.validate()
         handle_errors("Validation of collision detection failed")
 
     def get_parameter(self, name):
-        #"""Gets a single parameter from the collision detection."""
+        """Gets a single parameter from the collision detection."""
 
-        res = super(type(self), self).get_parameter(name)
+        res = super().get_parameter(name)
         return self._convert_param(name, res)
 
     def get_params(self):
         """Returns the parameters of the collision detection as dict.
 
         """
-        res = super(type(self), self).get_params()
+        res = super().get_params()
         for k in res.keys():
             res[k] = self._convert_param(k, res[k])
 

src/python/espressomd/comfixed.py

@@ -31,7 +31,7 @@ class ComFixed(ScriptInterfaceHelper):
     Parameters
     ----------
     types : array_like
-        List of types of which the center of mass
+        List of types for which the center of mass
         should be fixed.
     """