Some small fixes.

Author: ocefpaf

MANIFEST.in

@@ -1,2 +1,3 @@
 include *.txt
 include README.md
+recursive-include pysgrid *.py

README.md

@@ -2,4 +2,4 @@
 
 [![Build Status](https://travis-ci.org/sgrid/pysgrid.svg?branch=master)](https://travis-ci.org/sgrid/pysgrid)
 
-Python tools for sgrid
+Python tools for SGRID.

pysgrid/read_netcdf.py

@@ -70,8 +70,8 @@ def parse_padding(padding_str, mesh_topology_var):
         raw_dim, raw_sub_dim, raw_padding_var = padding_match
         dim = raw_dim.split(':')[0]
         sub_dim = raw_sub_dim
-        # Remove parentheses. (That is why regular expressions are bad!  You
-        # need a commend to explain what is going on.)
+        # Remove parentheses. (That is why regular expressions are bad!
+        # You need a commend to explain what is going on!!)
         cleaned_padding_var = re.sub('[\(\)]', '', raw_padding_var)
         # Get the padding value and remove spaces.
         padding_type = cleaned_padding_var.split(':')[1].strip()
@@ -124,11 +124,11 @@ def parse_vector_axis(variable_standard_name):
 
 class NetCDFDataset(object):
 
-    def __init__(self, nc_dataset_obj):
-        self.ncd = nc_dataset_obj
+    def __init__(self, nc):
+        self.nc = nc
         # in case a user as a version netcdf C library < 4.1.2
         try:
-            self._filepath = nc_dataset_obj.filepath()
+            self._filepath = nc.filepath()
         except ValueError:
             self._filepath = None
         self.sgrid_compliant_file()
@@ -139,7 +139,7 @@ def find_node_coordinates(self, node_dimensions):
         cell vertices.
 
         """
-        nc_vars = self.ncd.variables
+        nc_vars = self.nc.variables
         node_dims = node_dimensions.split(' ')
         node_dim_set = set(node_dims)
         x_node_coordinate = None
@@ -169,7 +169,7 @@ def find_node_coordinates(self, node_dimensions):
             return None
 
     def find_variables_by_attr(self, **kwargs):
-        nc_vars = self.ncd.variables
+        nc_vars = self.nc.variables
         matches = []
         keys = kwargs.keys()
         for nc_var in nc_vars.keys():
@@ -198,7 +198,7 @@ def find_coordinates_by_location(self, location_str, topology_dim):
         :param int topology_dim: the topology dimension of the grid
 
         """
-        nc_vars = self.ncd.variables
+        nc_vars = self.nc.variables
         vars_with_location = self.find_variables_by_attr(location=location_str)
         x_coordinate = None
         y_coordinate = None
@@ -276,7 +276,7 @@ def sgrid_compliant_file(self):
 
         """
         try:
-            find_grid_topology_var(self.ncd)
+            find_grid_topology_var(self.nc)
         except ValueError as e:
             raise e
 

pysgrid/sgrid.py

@@ -258,20 +258,20 @@ class SGridAttributes(object):
     attributes for either SGrid.
 
     """
-    def __init__(self, nc_dataset, topology_dim, topology_variable):
-        self.nc_dataset = nc_dataset
-        self.ncd = NetCDFDataset(self.nc_dataset)
+    def __init__(self, nc, topology_dim, topology_variable):
+        self.nc = nc
+        self.ncd = NetCDFDataset(self.nc)
         self.topology_dim = topology_dim
         self.topology_variable = topology_variable
-        self.topology_var = self.nc_dataset.variables[self.topology_variable]
+        self.topology_var = self.nc.variables[self.topology_variable]
 
     def get_dimensions(self):
-        ds_dims = self.nc_dataset.dimensions
+        ds_dims = self.nc.dimensions
         grid_dims = [(ds_dim, len(ds_dims[ds_dim])) for ds_dim in ds_dims]
         return grid_dims
 
     def get_topology_var(self):
-        grid_topology_var = find_grid_topology_var(self.nc_dataset)
+        grid_topology_var = find_grid_topology_var(self.nc)
         return grid_topology_var
 
     def get_attr_dimension(self, attr_name):
@@ -312,7 +312,7 @@ def get_node_coordinates(self):
     def get_variable_attributes(self, sgrid):
         dataset_variables = []
         grid_variables = []
-        nc_variables = self.nc_dataset.variables
+        nc_variables = self.nc.variables
         for nc_variable in nc_variables:
             nc_var = nc_variables[nc_variable]
             sgrid_var = SGridVariable.create_variable(nc_var, sgrid)
@@ -324,11 +324,8 @@ def get_variable_attributes(self, sgrid):
         sgrid.grid_variables = grid_variables
 
     def get_angles(self):
-        try:
-            # get angles if they exist, otherwise calculate them
-            grid_angles = self.nc_dataset.variables['angle'][:]
-            angles = grid_angles
-        except KeyError:
+        angles = self.nc.variables.get('angle')
+        if not angles:
             cell_centers = self.get_cell_center_lat_lon()
             centers_start = cell_centers[..., :-1, :]
             centers_end = cell_centers[..., 1:, :]
@@ -337,8 +334,8 @@ def get_angles(self):
 
     def get_cell_center_lat_lon(self):
         grid_cell_center_lon_var, grid_cell_center_lat_var = self.get_attr_coordinates('face_coordinates')  # noqa
-        grid_cell_center_lat = self.nc_dataset.variables[grid_cell_center_lat_var][:]  # noqa
-        grid_cell_center_lon = self.nc_dataset.variables[grid_cell_center_lon_var][:]  # noqa
+        grid_cell_center_lat = self.nc[grid_cell_center_lat_var]
+        grid_cell_center_lon = self.nc[grid_cell_center_lon_var]
         return pair_arrays(grid_cell_center_lon, grid_cell_center_lat)
 
     def get_cell_node_lat_lon(self):
@@ -347,8 +344,8 @@ def get_cell_node_lat_lon(self):
         except TypeError:
             cell_nodes = None
         else:
-            grid_cell_nodes_lat = self.nc_dataset.variables[grid_cell_nodes_lat_var][:]  # noqa
-            grid_cell_nodes_lon = self.nc_dataset.variables[grid_cell_nodes_lon_var][:]  # noqa
+            grid_cell_nodes_lat = self.nc[grid_cell_nodes_lat_var]
+            grid_cell_nodes_lon = self.nc[grid_cell_nodes_lon_var]
             cell_nodes = pair_arrays(grid_cell_nodes_lon, grid_cell_nodes_lat)
         return cell_nodes
 

pysgrid/utils.py

@@ -144,14 +144,14 @@ def infer_avg_axes(sgrid_obj, nc_var_obj):
             avg_dim = None
             continue
         else:
-            avg_dim = var_dim  # name of the dimension we're averaging over
-            break  # exit the loop once it's found
+            avg_dim = var_dim  # Name of the dimension we're averaging over.
+            break  # Exit the loop once it's found.
     if padding_info is not None and avg_dim is not None:
         var_position = var_dims.index(avg_dim)
         center_avg_axis = len(var_dims) - var_position - 1
     else:
         center_avg_axis = None
-    # define the node averaging axis for a variable
+    # Define the node averaging axis for a variable.
     if center_avg_axis == 1:
         node_avg_axis = 0
     elif center_avg_axis == 0:
@@ -202,7 +202,7 @@ def calculate_bearing(lon_lat_1, lon_lat_2):
 
 def calculate_angle_from_true_east(lon_lat_1, lon_lat_2):
     """
-    Return the angle from true east in radians
+    Return the angle from true east in radians.
 
     """
     bearing = calculate_bearing(lon_lat_1, lon_lat_2)
@@ -211,6 +211,5 @@ def calculate_angle_from_true_east(lon_lat_1, lon_lat_2):
     # Unsure if this is the appropriate thing to do for the last grid cell.
     angles = np.append(bearing_from_true_east_radians,
                        bearing_from_true_east_radians[..., -1:],
-                       axis=-1
-                       )
+                       axis=-1)
     return angles

requirements.txt

@@ -1,2 +1,2 @@
-netCDF4
+netCDF4 >=1.2.0
 numpy

setup.py

@@ -26,26 +26,25 @@ def readme():
     with open('README.md') as f:
         return f.read()
 
-setup(
-    name='pysgrid',
-    version=extract_version(),
-    description='Python package for working with staggered gridded data',
-    author='Andrew Yan',
-    author_email='[email protected]',
-    url='https://github.com/sgrid/pysgrid',
-    packages=find_packages(),
-    license='BSD',
-    long_description=readme(),
-    install_requires=reqs,
-    tests_require=['mock', 'nose'],
-    classifiers=[
-            'Development Status :: 3 - Alpha',
-            'Intended Audience :: Developers',
-            'Intended Audience :: Science/Research',
-            'License :: OSI Approved :: BSD License',
-            'Operating System :: POSIX :: Linux',
-            'Programming Language :: Python',
-            'Topic :: Scientific/Engineering',
-        ],
-    include_package_data=True,
-)
+setup(name='pysgrid',
+      version=extract_version(),
+      description='Python package for working with staggered gridded data',
+      author='Andrew Yan',
+      author_email='[email protected]',
+      url='https://github.com/sgrid/pysgrid',
+      packages=find_packages(),
+      license='BSD',
+      long_description=readme(),
+      install_requires=reqs,
+      tests_require=['mock', 'nose'],
+      classifiers=[
+          'Development Status :: 3 - Alpha',
+          'Intended Audience :: Developers',
+          'Intended Audience :: Science/Research',
+          'License :: OSI Approved :: BSD License',
+          'Operating System :: POSIX :: Linux',
+          'Programming Language :: Python',
+          'Topic :: Scientific/Engineering',
+          ],
+      include_package_data=True,
+      )