clean up a bunch of warnings

docs/.gitignore

@@ -1,2 +1,3 @@
 build
 _autosummary
+source/autoapi

docs/source/conf.py

@@ -31,6 +31,7 @@
 
 autoapi_type = 'python'
 autoapi_dirs = [ '../../opendrift' ]
+autoapi_keep_files = False  # set to True when debugging autoapi generated files
 
 extensions = [
         "sphinx_rtd_theme",

opendrift/elements/elements.py

@@ -1,17 +1,17 @@
 # This file is part of OpenDrift.
-# 
+#
 # OpenDrift is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, version 2
-# 
+#
 # OpenDrift is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with OpenDrift.  If not, see <http://www.gnu.org/licenses/>.
-# 
+#
 # Copyright 2015, Knut-Frode Dagestad, MET Norway
 
 from collections import OrderedDict
@@ -33,19 +33,20 @@ class LagrangianArray(object):
     types, e.g. oil, fish eggs...) to the core variables described below.
 
     Attributes:
+
         variables: An OrderedDict where keys are names of the
             variables/properties of the current object. The values
             of the OrderedDict are dictionaries with names such as
             'dtype', 'unit', 'standard_name' (CF), 'default' etc.
-        All variable names will be added dynamically as attributes of
+            All variable names will be added dynamically as attributes of
             the object after initialisation. These attributes will be
             numpy ndarrays of same length, or scalars. The core variables
             are:
         ID: an integer identifying each particle.
         status: 0 for active particles and a positive integer when deactivated
         lon: longitude (np.float32)
         lat: latitude (np.float32)
-        z: vertical position of the particle in m, 
+        z: vertical position of the particle in m,
             positive upwards (above sea surface)
     """
 
@@ -154,7 +155,7 @@ def extend(self, other):
             new_data = getattr(other, var)
 
             # If both arrays have an identical scalar, it remains a scalar
-            if (not isinstance(new_data, np.ndarray) and 
+            if (not isinstance(new_data, np.ndarray) and
                 not isinstance(present_data, np.ndarray) and
                 present_data == new_data):
                 continue

opendrift/models/basemodel.py

@@ -31,6 +31,7 @@
 
 import numpy as np
 import scipy
+import pyproj
 import configobj, validate
 try:
     import matplotlib
@@ -52,7 +53,7 @@
     print('matplotlib and/or cartopy is not available, can not make plots')
 
 import opendrift
-from opendrift.readers.basereader import pyproj, BaseReader, vector_pairs_xy
+from opendrift.readers.basereader import BaseReader, vector_pairs_xy
 from opendrift.readers import reader_from_url
 from opendrift.models.physics_methods import PhysicsMethods
 

opendrift/models/openberg.py

@@ -21,27 +21,19 @@
 import numpy as np
 import sys
 from scipy.interpolate import interp1d
-
-try:
-    from mpl_toolkits.basemap import Basemap
-    import matplotlib.pyplot as plt
-    from matplotlib import animation
-except:
-    logging.info('Basemap is not available, can not make plots')
-
+import pyproj
 
 from opendrift.models.basemodel import OpenDriftSimulation
 from opendrift.elements.elements import LagrangianArray
-from opendrift.readers.basereader import pyproj, BaseReader
-
+from opendrift.readers.basereader import BaseReader
 
 
 # Defining the iceberg element properties
 class IcebergObj(LagrangianArray):
     """Extending LagrangianArray with variables relevant for iceberg objects.
 
     """
-    
+
     # We add the properties to the element class
     variables = LagrangianArray.add_variables([
         ('wind_drift_factor', {'dtype': np.float32,				# The fraction of the wind speed at which an iceberg is moved
@@ -63,10 +55,10 @@ class OpenBerg(OpenDriftSimulation):
     """
 
     ElementType = IcebergObj
-    
+
     required_variables = ['x_wind', 'y_wind',
                           'x_sea_water_velocity', 'y_sea_water_velocity',
-                          'land_binary_mask'] 
+                          'land_binary_mask']
 
     fallback_values = {'x_wind': 0.0,
                        'y_wind': 0.0,
@@ -81,119 +73,119 @@ class OpenBerg(OpenDriftSimulation):
     def __init__(self, d=None, label=None, *args, **kwargs):
 
         self.name = 'OpenBerg'
-        self.label=label                                                                
-                
+        self.label=label
+
         self.required_profiles = ['x_sea_water_velocity',
                                   'y_sea_water_velocity']  # Get vertical current profiles
-                                  
+
         self.required_profiles_z_range = [-190, 0] # [min_depth, max_depth]
 
         # Calling general constructor of parent class
         super(OpenBerg, self).__init__(*args, **kwargs)
 
 
     def update(self):
-        """Update positions and properties of icebergs."""     
+        """Update positions and properties of icebergs."""
 		# Move icebergs at given % of wind speed
         self.advect_wind()
 
-        # Move icebergs as per Anne Barker et al, 2004, with weighted average of current  
+        # Move icebergs as per Anne Barker et al, 2004, with weighted average of current
         # down to draft of berg.
         # For current 10n meters down, where n is the depth index from 0 to 19
 
         # RETRIEVE CURRENT SPEED:
         y_sea_water_vel = self.environment_profiles['y_sea_water_velocity']
-        x_sea_water_vel = self.environment_profiles['x_sea_water_velocity']        
+        x_sea_water_vel = self.environment_profiles['x_sea_water_velocity']
 
-		# FIND THE WEIGHTED AVERAGE CURRENT SPEED ACROSS THE ICEBERG KEEL        
+		# FIND THE WEIGHTED AVERAGE CURRENT SPEED ACROSS THE ICEBERG KEEL
         net_x_swv = np.zeros(x_sea_water_vel.shape[1])
         net_y_swv = np.zeros(y_sea_water_vel.shape[1])
         for indx in range(len(self.uw_weighting)):
             net_y_swv = net_y_swv +y_sea_water_vel[indx,:]*self.uw_weighting[indx]
             net_x_swv = net_x_swv +x_sea_water_vel[indx,:]*self.uw_weighting[indx]
-            
+
         self.update_positions(net_x_swv,net_y_swv)
-            
+
 
     def prepare_run(self):
         """	Model spesific preparations.
          	Set the weighting for modelled current depths as per Table 5 of Barker 2004,
         	'Determination of Iceberg Draft, Mass and Cross-Sectional Areas',
-        	Proceedings of The Fourteenth (2004) International Offshore and 
+        	Proceedings of The Fourteenth (2004) International Offshore and
         	Polar Engineering Conference.
-        	
+
         	NB! This version of OpenBerg does not allow for seeding of iceberg elements
         	of different sizes.
-        	
+
         	Also controles that the model handles readers without block data correctly.
         """
-        # Retrieve profile provided in z dimension by reader  
+        # Retrieve profile provided in z dimension by reader
         variable_groups, reader_groups, missing_variables = \
-         	self.get_reader_groups(['x_sea_water_velocity','y_sea_water_velocity']) 
-        
+         	self.get_reader_groups(['x_sea_water_velocity','y_sea_water_velocity'])
+
         if len(reader_groups) == 0:
         	# No current data -> fallback values used
         	self.uw_weighting = np.array([1])
-        	return 
-        	
+        	return
+
 		# Obtain depth levels from reader:
         reader_name = reader_groups[0][0]
         profile = np.abs(np.ma.filled(self.readers[reader_name].z))
-        
-       # Make sure that interpolation is left to reader if no blocks are used . 
-       # NB! This is a workaround, two additional points should be removed in basereader!      
+
+       # Make sure that interpolation is left to reader if no blocks are used .
+       # NB! This is a workaround, two additional points should be removed in basereader!
         if self.readers[reader_name].return_block == False:
         	self.use_block = False
-        
+
         # If current data is missing in at least one dimension, no weighting is performed:
         if len(missing_variables) > 0:
         	logging.warning('Missing current data, weigthing array set to [1]')
         	self.uw_weighting = np.array([1])
-        	return       
-        	  		
+        	return
+
         # No need to create weighting array if only one z-level is provided:
         if len(profile) == 1:
         	self.uw_weighting = np.array([1])
         	return
-        	        	
+
         # Make copies to prevent outside value to be modified
         water_line_length = self.elements_scheduled.water_line_length.copy()
         depth = self.elements_scheduled.keel_depth.copy()
 
         # Calculate the weighting array corresponding to the iceberg profile
         uw_weighting = self.composite_iceberg(water_line_length=water_line_length, depth=depth)
-
 
-
+
+
         #### Interpolate weighting array to match z-dimension of current reader ###
-        
+
         # Array of "Barker-depths" (10n)m, , where n is the depth index from 0 to 19
-        x = np.linspace(0,(len(uw_weighting)-1)*10,len(uw_weighting)) 
-        
+        x = np.linspace(0,(len(uw_weighting)-1)*10,len(uw_weighting))
+
         # Create a linear interpolator
-        interpol = interp1d(x,uw_weighting) 
-        
-        # Obtain corresponding depth levels from reader:        
+        interpol = interp1d(x,uw_weighting)
+
+        # Obtain corresponding depth levels from reader:
         self.reader_z_profile = profile[(profile >= 0) & (profile <= x.max())]
-        
+
         if len(profile[profile < 0]) > 0:
         	logging.warning('Current reader containing currents above water!'
         						'Weighting of current profile may not work!')
-        
+
         # Interpolate and normalize weights:
-        
-        ###### NB!  Interpolator only includes values from reader within the range of the 
+
+        ###### NB!  Interpolator only includes values from reader within the range of the
         ######		Barker-depth array. Meaning values just outside is not used for interpolation.
-        ######		Ex.: If x.max=195 and the current reader includes data for 
-        ######		the z-profile: [0,3,10,15,25,50,75,100,150,200] only data from the 
+        ######		Ex.: If x.max=195 and the current reader includes data for
+        ######		the z-profile: [0,3,10,15,25,50,75,100,150,200] only data from the
         ######		z-levels [0,3,10,15,25,50,75,100,150] are used.
-        
-        interpol_weight = interpol(self.reader_z_profile) 
+
+        interpol_weight = interpol(self.reader_z_profile)
         normalized_weight = interpol_weight/interpol_weight.sum()
-        
+
         if normalized_weight.all():
             self.uw_weighting = normalized_weight
-                              	
+
         super(OpenBerg, self).prepare_run()
 
     def composite_iceberg(self, water_line_length=90.5, depth=60):
@@ -203,30 +195,30 @@ def composite_iceberg(self, water_line_length=90.5, depth=60):
     		in table 5 from Barker et. al.(2004).
     	"""
 		# Parameters from Baker et. al.:
-		
+
     	a_param = [9.5173,11.1717,12.4798,13.6010,14.3249,13.7432,13.4527,15.7579,
     				14.7259,11.8195,11.3610,10.9202,10.4966,10.0893,9.6979,9.3216,8.9600,
     				8.6124,8.2783,7.9571]
-				
+
     	b_param = [-25.94,-107.50,-232.01,-344.60,-456.57,-433.33,-519.56,-1111.57,-1125.00,
     					-852.90,-931.48,-1007.02,-1079.62,-1149.41,-1216.49,-1280.97,
     					-1342.95,-1402.52,-1459.78,-1514.82]
-				
+
     	d = int(round(depth/10))
 
     	if d < 0: #Incase depth is given as a negative value
-    		d = -d 
+    		d = -d
 
 
     	if d > len(a_param):
     		d = len(a_param)
     		print('##### OpenBerg does not support icebergs with keel depths greater than 200m!\n' +
-				'Using a composite iceberg with given waterline length and keel depth 200m')  
+				'Using a composite iceberg with given waterline length and keel depth 200m')
 
     	area_list=[]
 
     	for i in range(0,d):
-	
+
     		A = self.lin_func(a_param[i],b_param[i],water_line_length)
     		area_list.append(A)
 
@@ -237,10 +229,10 @@ def composite_iceberg(self, water_line_length=90.5, depth=60):
     	weigthing_array = np.array(area_list)/sum(np.array(area_list))
 
     	return weigthing_array
-	
-	
+
+
     def lin_func(self,a,b,L):
     	"""Returns value of linear function A=aL+b."""
     	A = a*L + b
-	
+
     	return A

opendrift/models/openoil.py

@@ -19,12 +19,12 @@
 import numpy as np
 from datetime import datetime
 import logging
+import pyproj
 import matplotlib.pyplot as plt
 
 from opendrift.models.basemodel import OpenDriftSimulation
 from opendrift.elements import LagrangianArray
 import opendrift.models.noaa_oil_weathering as noaa
-from opendrift.readers.basereader import pyproj
 
 try:
     from itertools import izip as zip
@@ -191,7 +191,7 @@ def __init__(self, weathering_model='default', *args, **kwargs):
 
         self.oil_weathering_model = weathering_model
 
-        # Update config with oiltypes 
+        # Update config with oiltypes
         oiltypes = [str(a) for a in self.oiltypes]
         self._add_config('seed:oil_type', oiltypes,
                          'Oil type', overwrite=True)
@@ -219,7 +219,7 @@ def update_surface_oilfilm_thickness(self):
         # Using stereographic coordinates to get regular X and Y
         psproj = pyproj.Proj(
             '+proj=stere +lat_0=%s +lat_ts=%s +lon_0=%s' %
-            (meanlat, meanlat, meanlon)) 
+            (meanlat, meanlat, meanlon))
         X,Y = psproj(self.elements.lon[surface], self.elements.lat[surface])
         mass_bin, x_edge, y_edge, binnumber = binned_statistic_2d(
             X, Y, self.elements.mass_oil[surface],
@@ -446,7 +446,7 @@ def prepare_run(self):
 
             self.oil_water_interfacial_tension = \
                 self.oiltype.oil_water_surface_tension()[0]
-            logging.info('Oil-water surface tension is %f Nm' % 
+            logging.info('Oil-water surface tension is %f Nm' %
                          self.oil_water_interfacial_tension)
         else:
             logging.info('Using default oil-water tension of 0.03Nm')
@@ -1007,7 +1007,7 @@ def seed_from_geotiff_thickness(self, filename, number=50000,
                                 'using present time: %s' % time)
 
         ds = gdal.Open(filename)
-        
+
         srcband = ds.GetRasterBand(1)
         data = srcband.ReadAsArray()
 
@@ -1059,7 +1059,7 @@ def seed_from_geotiff_thickness(self, filename, number=50000,
             total_area[cat-1] = np.sum(areas)
             layers[cat-1].DeleteFeature(outer)
             layers[cat-1].ResetReading()
-            
+
         # Calculate how many elements to be seeded for each category
         areas_weighted = total_area*thickness_microns
         numbers = number*areas_weighted/np.sum(areas_weighted)