Merge pull request #221 from stoiver/anuga_py3

Anuga py3

.travis.yml

@@ -7,19 +7,19 @@ matrix:
          language: generic
          sudo: false
          python: "2.7"
-         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="false"  DISTRIB="conda_macos"
+         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="conda"  PYPAR_AVAILABLE="mpi4py" DISTRIB="conda_macos"
 
        - os: linux
          language: generic
          sudo: required
          python: "2.7"
-         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="openmpi"  DISTRIB="conda"
+         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="conda"  PYPAR_AVAILABLE="mpi4py" DISTRIB="conda"
 
        - os: linux
          dist: trusty
          sudo: required
          python: "2.7_with_system_site_packages"
-         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="mpich"  DISTRIB="ubuntu"
+         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="mpich"  PYPAR_AVAILABLE="mpi4py" DISTRIB="ubuntu"
 
        - os: linux
          dist: trusty
@@ -31,7 +31,7 @@ matrix:
          dist: trusty
          sudo: required
          python: "2.7_with_system_site_packages"
-         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="openmpi"  DISTRIB="ubuntu" COVERAGE="--coverage"
+         env: PYTHON_VERSION="2.7"  ANUGA_PARALLEL="openmpi"  PYPAR_AVAILABLE="mpi4py" DISTRIB="ubuntu" COVERAGE="--coverage"
 
 
 install:

anuga/abstract_2d_finite_volumes/ermapper_grids.py

@@ -207,39 +207,39 @@ def create_default_header(header = {}):
     #           to be filled with default values
 
 
-    if not header.has_key('datum'):
+    if 'datum' not in header:
         header['datum'] = '"GDA94"'
-    if not header.has_key('projection'):
+    if 'projection' not in header:
         header['projection'] = '"GEOGRAPHIC"'
-    if not header.has_key('coordinatetype'):
+    if 'coordinatetype' not in header:
         header['coordinatetype'] = 'LL'
-    if not header.has_key('rotation'):
+    if 'rotation' not in header:
         header['rotation'] = '0:0:0.0'
-    if not header.has_key('units'):
+    if 'units' not in header:
         header['units'] = '"METERS"'
-    if not header.has_key('celltype'):
+    if 'celltype' not in header:
         header['celltype'] = 'IEEE4ByteReal'
-    if not header.has_key('nullcellvalue'):
+    if 'nullcellvalue' not in header:
         header['nullcellvalue'] = '-99999'
-    if not header.has_key('xdimension'):
+    if 'xdimension' not in header:
         header['xdimension'] = '100'
-    if not header.has_key('latitude'):
+    if 'latitude' not in header:
         header['latitude'] = '0:0:0'
-    if not header.has_key('longitude'):
+    if 'longitude' not in header:
         header['longitude'] = '0:0:0'
-    if not header.has_key('ydimension'):
+    if 'ydimension' not in header:
         header['ydimension'] = '100'
-    if not header.has_key('nroflines'):
+    if 'nroflines' not in header:
         header['nroflines'] = '3'
-    if not header.has_key('nrofcellsperline'):
+    if 'nrofcellsperline' not in header:
         header['nrofcellsperline'] = '4'
-    if not header.has_key('registrationcellx'):
+    if 'registrationcellx' not in header:
         header['registrationcellx'] = '0'
-    if not header.has_key('registrationcelly'):
+    if 'registrationcelly' not in header:
         header['registrationcelly'] = str(int(header['nroflines'])-1)
-    if not header.has_key('nrofbands'):
+    if 'nrofbands' not in header:
         header['nrofbands'] = '1'
-    if not header.has_key('value'):
+    if 'value' not in header:
         header['value'] = '"Default_Band"'
 
 

anuga/abstract_2d_finite_volumes/file_function.py

@@ -134,8 +134,7 @@ def file_function(filename,
                              compression=False,                  
                              verbose=verbose)
     else:
-        f, starttime = apply(_file_function,
-                             args, kwargs)
+        f, starttime = _file_function(*args, **kwargs)
 
     #FIXME (Ole): Pass cache arguments, such as compression, in some sort of
     #structure
@@ -268,7 +267,7 @@ def get_netcdf_file_function(filename,
     # are present in file 
     missing = []
     for quantity in ['time'] + quantity_names:
-        if not fid.variables.has_key(quantity):
+        if quantity not in fid.variables:
             missing.append(quantity)
 
     if len(missing) > 0:
@@ -280,7 +279,7 @@ def get_netcdf_file_function(filename,
     # Decide whether this data has a spatial dimension
     spatial = True
     for quantity in ['x', 'y']:
-        if not fid.variables.has_key(quantity):
+        if quantity not in fid.variables:
             spatial = False
 
     if filename[-3:] == 'tms' and spatial is True:

anuga/abstract_2d_finite_volumes/gauge.py

@@ -7,12 +7,13 @@
    Ole Nielsen, Stephen Roberts, Duncan Gray, Christopher Zoppou, James Hudson
    Geoscience Australia
 """
+from __future__ import absolute_import
 
 import numpy as num
 
 from anuga.geospatial_data.geospatial_data import ensure_absolute
-from util import check_list, calc_bearing
-from file_function import file_function
+from .util import check_list, calc_bearing
+from .file_function import file_function
 
 import os
 
@@ -142,7 +143,7 @@ def sww2csv_gauges(sww_file,
 
     try:
         point_reader = reader(file(gauge_file))
-    except Exception, e:
+    except Exception as e:
         msg = 'File "%s" could not be opened: Error="%s"' % (gauge_file, e)
         raise Exception(msg)
 
@@ -411,7 +412,7 @@ def _sww2timeseries(swwfiles,
 
     try:
         fid = open(gauge_filename)
-    except Exception, e:
+    except Exception as e:
         msg = 'File "%s" could not be opened: Error="%s"' % (gauge_filename, e)
         raise Exception(msg)
 
@@ -449,7 +450,7 @@ def _sww2timeseries(swwfiles,
     for swwfile in swwfiles.keys():
         try:
             fid = open(swwfile)
-        except Exception, e:
+        except Exception as e:
             msg = 'File "%s" could not be opened: Error="%s"' % (swwfile, e)
             raise Exception(msg)
 
@@ -515,7 +516,7 @@ def _sww2timeseries(swwfiles,
     if verbose and len(gauge_index) > 0:
          log.critical('Inputs OK - going to generate figures')
 
-    if len(gauge_index) <> 0:
+    if len(gauge_index) != 0:
         texfile, elev_output = \
             _generate_figures(plot_quantity, file_loc, report, reportname,
                              surface, leg_label, f_list, gauges, locations,

anuga/abstract_2d_finite_volumes/general_mesh.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 import copy
 import numpy as num
 
@@ -799,7 +800,7 @@ def build_inverted_triangle_structure(self):
 
         if number_of_orphan_nodes > 0 and self.verbose:
             msg = 'Node(s) %d not associated to a triangle.' % orphan_nodes[0]
-            print msg
+            print(msg)
 
         if number_of_lone_nodes > 0:
             number_of_triangles_per_node =  \

anuga/abstract_2d_finite_volumes/generic_boundary_conditions.py

@@ -99,9 +99,9 @@ def get_boundary_values(self, t=None):
 
         try:
             res = self.function(t)
-        except Modeltime_too_early, e:
+        except Modeltime_too_early as e:
             raise Modeltime_too_early(e)
-        except Modeltime_too_late, e:
+        except Modeltime_too_late as e:
             if self.default_boundary is None:
                 raise Modeltime_too_late(e) # Reraise exception
             else:
@@ -328,7 +328,7 @@ def __init__(self, domain=None,
 
         try:
             q = function(0.0)
-        except Exception, e:
+        except Exception as e:
             msg = 'Function for time boundary could not be executed:\n%s' %e
             raise Exception(msg)
 
@@ -447,7 +447,7 @@ def __init__(self, domain=None,
 
         try:
             q = function(0.0, 0.0, 0.0)
-        except Exception, e:
+        except Exception as e:
             msg = 'Function for time_space_boundary could not be executed:\n%s' %e
             raise Exception(msg)
 
@@ -481,9 +481,9 @@ def evaluate(self, vol_id=None, edge_id=None):
 
         try:
             res = self.function(self.domain.get_time(), x, y)
-        except Modeltime_too_early, e:
+        except Modeltime_too_early as e:
             raise Modeltime_too_early(e)
-        except Modeltime_too_late, e:
+        except Modeltime_too_late as e:
             if self.default_boundary is None:
                 raise Exception(e) # Reraise exception
             else:
@@ -656,9 +656,9 @@ def evaluate(self, vol_id=None, edge_id=None):
 
             try:
                 res = self.F(t, point_id=i)
-            except Modeltime_too_early, e:
+            except Modeltime_too_early as e:
                 raise Modeltime_too_early(e)
-            except Modeltime_too_late, e:
+            except Modeltime_too_late as e:
                 if self.default_boundary is None:
                     raise Exception(e) # Reraise exception
                 else:

anuga/abstract_2d_finite_volumes/generic_domain.py

@@ -11,15 +11,17 @@
    Ole Nielsen, Stephen Roberts, Duncan Gray
    Geoscience Australia
 """
+from __future__ import print_function
+from __future__ import absolute_import
 
 from time import time as walltime
 
 from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh
-from pmesh2domain import pmesh_to_domain
-from tag_region import Set_tag_region as region_set_tag_region
+from .pmesh2domain import pmesh_to_domain
+from .tag_region import Set_tag_region as region_set_tag_region
 from anuga.geometry.polygon import inside_polygon
 from anuga.abstract_2d_finite_volumes.util import get_textual_float
-from quantity import Quantity
+from .quantity import Quantity
 import anuga.utilities.log as log
 
 import numpy as num
@@ -457,7 +459,7 @@ def statistics(self, *args, **kwargs):
         return self.mesh.statistics(*args, **kwargs)
 
     def print_statistics(self, *args, **kwargs):
-        print self.statistics(*args, **kwargs)
+        print(self.statistics(*args, **kwargs))
 
     def get_extent(self, *args, **kwargs):
         return self.mesh.get_extent(*args, **kwargs)    
@@ -707,7 +709,7 @@ def set_quantity(self, name,
         """
 
         # Do the expression stuff
-        if kwargs.has_key('expression'):
+        if 'expression' in kwargs:
             expression = kwargs['expression']
             del kwargs['expression']
 
@@ -727,7 +729,7 @@ def add_quantity(self, name,
         """
 
         # Do the expression stuff
-        if kwargs.has_key('expression'):
+        if 'expression' in kwargs:
             expression = kwargs['expression']
             Q2 = self.create_quantity_from_expression(expression)
         else:
@@ -751,7 +753,7 @@ def minimum_quantity(self, name,
         """
 
         # Do the expression stuff
-        if kwargs.has_key('expression'):
+        if 'expression' in kwargs:
             expression = kwargs['expression']
             Q2 = self.create_quantity_from_expression(expression)
         else:
@@ -775,7 +777,7 @@ def maximum_quantity(self, name,
         """
 
         # Do the expression stuff
-        if kwargs.has_key('expression'):
+        if 'expression' in kwargs:
             expression = kwargs['expression']
             Q2 = self.create_quantity_from_expression(expression)
         else:
@@ -898,7 +900,7 @@ def set_boundary(self, boundary_map):
         for k, (vol_id, edge_id) in enumerate(x):
             tag = self.boundary[(vol_id, edge_id)]
 
-            if self.boundary_map.has_key(tag):
+            if tag in self.boundary_map:
                 B = self.boundary_map[tag]  # Get callable boundary object
 
                 if B is not None:
@@ -1208,12 +1210,12 @@ def timestepping_statistics(self, track_speeds=False,
         return msg
 
     def print_timestepping_statistics(self, *args, **kwargs):
-        print self.timestepping_statistics(self, *args, **kwargs)
+        print(self.timestepping_statistics(self, *args, **kwargs))
 
 
 
     def print_boundary_statistics(self, quantities=None, tags=None):
-        print self.boundary_statistics(quantities, tags)
+        print(self.boundary_statistics(quantities, tags))
 
     def write_boundary_statistics(self, quantities=None, tags=None):
         log.critical(self.boundary_statistics(quantities, tags))
@@ -1450,7 +1452,7 @@ def get_starttime(self):
     def set_starttime(self, time):
 
         if self.evolved_called: 
-            raise "Can't change simulation start time once evolve has been called"
+            raise Exception("Can't change simulation start time once evolve has been called")
 
         self.starttime = float(time)
         self.set_time(0.0)
@@ -1476,7 +1478,7 @@ def dump_triangulation(self, filename="domain.png"):
             import matplotlib.pyplot as plt
             import matplotlib.tri as tri
         except:
-            print "Couldn't import module from matplotlib, probably you need to update matplotlib"
+            print("Couldn't import module from matplotlib, probably you need to update matplotlib")
             raise
 
         vertices = self.get_vertex_coordinates()
@@ -2284,7 +2286,7 @@ def update_ghosts(self, quantities=None):
 
         #Update of ghost cells
         iproc = self.processor
-        if self.full_send_dict.has_key(iproc):
+        if iproc in self.full_send_dict:
 
             # now store full as local id, global id, value
             Idf  = self.full_send_dict[iproc][0]

anuga/abstract_2d_finite_volumes/mesh_factory.py

@@ -1,6 +1,7 @@
 """Library of standard meshes and facilities for reading various
 mesh file formats
 """
+from __future__ import absolute_import
 
 import anuga.utilities.log as log
 import numpy as num
@@ -165,7 +166,7 @@ def rectangular_cross(m, n, len1=1.0, len2=1.0, origin = (0.0, 0.0)):
     points = num.empty([(m+1)*(n+1)+m*n,2], dtype=num.float)
     elements = num.empty([4*m*n,3], dtype=num.int)
 
-    from mesh_factory_ext import rectangular_cross_construct
+    from .mesh_factory_ext import rectangular_cross_construct
     boundary = rectangular_cross_construct(arrParams, arrOrigin, points, elements)
 
     #points = list(arrPoints)