formatting of the doc

smrt/inputs/make_medium.py

@@ -117,25 +117,25 @@ def make_snowpack(thickness,
                   atmosphere=None,
                   **kwargs):
     """
-    build a multi-layered snowpack. Each parameter can be an array, list or a constant value.
+    Build a multi-layered snowpack. Each parameter can be an array, list or a constant value.
 
     :param thickness: thicknesses of the layers in meter (from top to bottom). The last layer thickness can be "numpy.inf"
-    for a semi-infinite layer.
+        for a semi-infinite layer.
     :param microstructure_model: microstructure_model to use (e.g. sticky_hard_spheres or independent_sphere or exponential).
     :param surface: type of surface interface, flat/fresnel is the default.  If surface and interface are both set,
-    the interface must be a constant refering to all the "internal" interfaces.
+        the interface must be a constant refering to all the "internal" interfaces.
     :param interface: type of interface, flat/fresnel is the default. It is usually a string for the interfaces
-    without parameters (e.g. Flat or Transparent) or is created with :py:func:`~smrt.core.interface.make_interface` in more complex cases.
-    Interface can be a constant or a list. In the latter case, its length must be the same as the number of layers,
-    and interface[0] refers to the surface interface.
+        without parameters (e.g. Flat or Transparent) or is created with :py:func:`~smrt.core.interface.make_interface` in more complex cases.
+        Interface can be a constant or a list. In the latter case, its length must be the same as the number of layers,
+        and interface[0] refers to the surface interface.
     :param density: densities of the layers.
     :param substrate: set the substrate of the snowpack. Another way to add a substrate is to use the + operator
-    (e.g. snowpack + substrate).
+        (e.g. snowpack + substrate).
     :param **kwargs: All the other parameters (temperature, microstructure parameters, emmodel, etc.) are given as optional arguments
-    (e.g. temperature=[270, 250]).
-    They are passed for each layer to the function :py:func:`~smrt.inputs.make_medium.make_snow_layer`.
-    Thus, the documentation of this function is the reference. It describes precisely the available parameters.
-    The microstructure parameter(s) depend on the microstructure_model used and is documented in each microstructure_model module.
+        (e.g. temperature=[270, 250]).
+        They are passed for each layer to the function :py:func:`~smrt.inputs.make_medium.make_snow_layer`.
+        Thus, the documentation of this function is the reference. It describes precisely the available parameters.
+        The microstructure parameter(s) depend on the microstructure_model used and is documented in each microstructure_model module.
 
     e.g.::
 
@@ -190,12 +190,12 @@ def make_snow_layer(layer_thickness,
     :param background_permittivity_model: permittivity formulation for the background (default is air).
     :param volumetric_liquid_water: volume of liquid water with respect to the volume of snow (default=0).
     :param liquid_water: May be depreciated in the future (use instead volumetric_liquid_water): volume of liquid water 
-    with respect to ice+water volume (default=0). liquid_water = water_volume / (ice_volume + water_volume).
+        with respect to ice+water volume (default=0). liquid_water = water_volume / (ice_volume + water_volume).
     :param salinity: salinity in kg/kg, for using PSU as unit see PSU constant in smrt module (default = 0).
     :param medium: indicate which medium the layer is made of ("snow" is a default). 
-    It is used when emmodel is a dictionary mapping from medium to emmodels in :py:func:`~smrt.core.model.make_model`
+        It is used when emmodel is a dictionary mapping from medium to emmodels in :py:func:`~smrt.core.model.make_model`
     :param kwargs: other microstructure parameters are given as optional arguments (in Python words) but may be required (in SMRT words).
-    See the documentation of the microstructure model.
+        See the documentation of the microstructure model.
 
     :returns: :py:class:`SnowLayer` instance
 """
@@ -335,25 +335,25 @@ def make_ice_column(ice_type,
 
     :param ice_type: Ice type. Options are "firstyear", "multiyear", "fresh"
     :param thickness: thicknesses of the layers in meter (from top to bottom). The last layer thickness can be "numpy.inf"
-    for a semi-infinite layer.
+        for a semi-infinite layer.
     :param temperature: temperature of ice/water in K
     :param brine_inclusion_shape: assumption for shape of brine inclusions. So far, "spheres" or "random_needles"
-    (i.e. elongated ellipsoidal inclusions), and "mix" (a mix of the two) are implemented.
+        (i.e. elongated ellipsoidal inclusions), and "mix" (a mix of the two) are implemented.
     :param salinity: salinity of ice/water in kg/kg (see PSU constant in smrt module). Default is 0. If neither salinity
-    nor brine_volume_fraction are given, the ice column is considered to consist of fresh water ice.
+        nor brine_volume_fraction are given, the ice column is considered to consist of fresh water ice.
     :param brine_volume_fraction: brine / liquid water fraction in sea ice, optional parameter, if not given brine volume fraction is
-    calculated from temperature and salinity in ~.smrt.permittivity.brine_volume_fraction
+        calculated from temperature and salinity in ~.smrt.permittivity.brine_volume_fraction
     :param density: density of ice layer in kg m :sup:`-3`
     :param porosity: porosity of ice layer (0 - 1). Default is 0.
     :param add_water_substrate: Adds a substrate made of water below the ice column.
-    Possible arguments are True (default) or False. If True looks for ice_type to determine if a saline or fresh water layer is
-    added and/or uses the optional arguments 'water_temperature', 'water_salinity' of the water substrate.
+        Possible arguments are True (default) or False. If True looks for ice_type to determine if a saline or fresh water layer is
+        added and/or uses the optional arguments 'water_temperature', 'water_salinity' of the water substrate.
     :param surface: type of surface interface, flat/fresnel is the default.  If surface and interface are both set, the interface must be
-    a constant refering to all the "internal" interfaces.
+        a constant refering to all the "internal" interfaces.
     :param interface: type of interface, flat/fresnel is the default. It is usually a string for the interfaces without parameters
-    (e.g. Flat or Transparent) or is created with :py:func:`~smrt.core.interface.make_interface` in more complex cases.
-    Interface can be a constant or a list. In the latter case, its length must be the same as the number of layers,
-    and interface[0] refers to the surface interface.
+        (e.g. Flat or Transparent) or is created with :py:func:`~smrt.core.interface.make_interface` in more complex cases.
+        Interface can be a constant or a list. In the latter case, its length must be the same as the number of layers,
+        and interface[0] refers to the surface interface.
     :param substrate: if add_water_substrate is False, the substrate can be prescribed with this argument.
 
     All the other optional arguments are passed for each layer to the function :py:func:`~smrt.inputs.make_medium.make_ice_layer`.
@@ -428,19 +428,19 @@ def make_ice_layer(ice_type,
     :param temperature: temperature of layer in K
     :param salinity: (firstyear and multiyear) salinity in kg/kg (see PSU constant in smrt module)
     :param brine_inclusion_shape: (firstyear and multiyear) assumption for shape of brine inclusions (so far,
-    "spheres" and "random_needles" (i.e. elongated ellipsoidal inclusions), and "mix_spheres_needles" are implemented)
+        "spheres" and "random_needles" (i.e. elongated ellipsoidal inclusions), and "mix_spheres_needles" are implemented)
     :param brine_volume_fraction: (firstyear and multiyear) brine / liquid water fraction in sea ice, optional parameter,
-    if not given brine volume fraction is calculated from temperature and salinity in ~.smrt.permittivity.brine_volume_fraction
+        if not given brine volume fraction is calculated from temperature and salinity in ~.smrt.permittivity.brine_volume_fraction
     :param density: (multiyear) density of ice layer in kg m :sup:`-3`. If not given, density is calculated from temperature,
-    salinity and ice porosity.
+        salinity and ice porosity.
     :param porosity: (mutliyear and fresh) air porosity of ice layer (0..1). Default is 0.
     :param ice_permittivity_model: (all) pure ice permittivity formulation (default is ice_permittivity_matzler06)
     :param brine_permittivity_model: (firstyear and multiyear) brine permittivity formulation (default is brine_permittivity_stogryn85)
     :param saline_ice_permittivity_model: (multiyear) model to mix ice and brine. The default uses polder van staten and
-    ice_permittivity_model and brine_permittivity_model. It is highly recommanded to use the default.
+        ice_permittivity_model and brine_permittivity_model. It is highly recommanded to use the default.
     :param kwargs: other microstructure parameters are given as optional arguments (in Python words) but may be required (in SMRT words).
     :param medium: indicate which medium the layer is made of ("ice" is a default). 
-    It is used when emmodel is a dictionary mapping from medium to emmodels in :py:func:`~smrt.core.model.make_model`
+        It is used when emmodel is a dictionary mapping from medium to emmodels in :py:func:`~smrt.core.model.make_model`
 
     See the documentation of the microstructure model.
 
@@ -615,7 +615,7 @@ def water_parameters(ice_type, **kwargs):
     """Make a semi-infinite water layer.
 
     :param ice_type: ice_type is used to determine if a saline or fresh water layer is added
-    Optional arguments are 'water_temperature', 'water_salinity' and 'water_depth' of the water layer.
+    The optional arguments are 'water_temperature', 'water_salinity' and 'water_depth' of the water layer.
     """
 
     # prepare default
@@ -690,7 +690,7 @@ def make_generic_stack(thickness, temperature=273, ks=0, ka=0, effective_permitt
     Must be used with presribed_kskaeps emmodel.
 
     :param thickness: thicknesses of the layers in meter (from top to bottom). The last layer thickness can be "numpy.inf" for
-    a semi-infinite layer.
+        a semi-infinite layer.
     :param temperature: temperature of layers in K
     :param ks: scattering coefficient of layers in m^-1
     :param ka: absorption coefficient of layers in m^-1

smrt/permittivity/ice.py

@@ -106,7 +106,7 @@ def ice_permittivity_maetzler87(frequency, temperature):
 """
 
     import warnings
-    
+
     freqGHz = frequency / 1e9
     # Equation 10
     Ereal = 3.1884 + 9.1e-4 * (temperature - FREEZING_POINT)
@@ -155,8 +155,8 @@ def ice_permittivity_tiuri84(frequency, temperature):
 
     # Eq (6) - Imaginary part
     Eimag = 1.59e6 * \
-            (0.52 * density_gm3 + 0.62*density_gm3**2) * \
-            (frequency**-1 + 1.23e-14 * frequency**.5) * math.exp(0.036 * temp_degC)
+        (0.52 * density_gm3 + 0.62*density_gm3**2) * \
+        (frequency**-1 + 1.23e-14 * frequency**.5) * math.exp(0.036 * temp_degC)
 
     return Ereal + 1j * Eimag
 
@@ -196,7 +196,6 @@ def _ice_permittivity_DMRTML(frequency, temperature):
     # Only use if invoking an exact DMRT-ML simulation.
     # Should not be included in the sphinx documentation
 
-
     # Raise exception if temperature is zero
     # if temperature == 0:
     #     raise SMRTError('Temperature used in calculation of ice permittivity is zero')

smrt/permittivity/saline_ice.py

@@ -48,18 +48,22 @@ def impure_ice_permittivity_maetzler06(frequency, temperature, salinity):
 
 
 @layer_properties("temperature", "brine_volume_fraction",
-                   optional=("brine_inclusion_shape", "brine_mixing_ratio", "ice_permittivity_model", "brine_permittivity_model"))
-
+                  optional=("brine_inclusion_shape", "brine_mixing_ratio", "ice_permittivity_model", "brine_permittivity_model"))
 def saline_ice_permittivity_pvs_mixing(frequency, temperature, brine_volume_fraction, brine_inclusion_shape='spheres',
                                        brine_mixing_ratio=1, ice_permittivity_model=None, brine_permittivity_model=None):
     """Computes effective permittivity of saline ice using the Polder Van Santen mixing formulaes.
 
         :param frequency: frequency in Hz
         :param temperature: ice temperature in K
         :param brine_volume_fraction: brine / liquid water fraction in sea ice
-        :param brine_inclusion_shape: Assumption for shape(s) of brine inclusions. Can be a string for single shape, or a list/tuple/dict of strings for mixture of shapes. So far, we have the following shapes: "spheres" and "random_needles" (i.e. randomly-oriented elongated ellipsoidal inclusions). 
-            If the argument is a dict, the keys are the shapes and the values are the mixing ratio. If it is a list, the mixing_ratio argument is required.
-        :param brine_mixing_ratio: The mixing ratio of the shapes. This is only relevant when inclusion_shape is a list/tuple. Mixing ratio must be a sequence with length len(inclusion_shape)-1. The mixing ratio of the last shapes is deduced as the sum of the ratios must equal to 1.
+        :param brine_inclusion_shape: Assumption for shape(s) of brine inclusions. Can be a string for single shape,
+            or a list/tuple/dict of strings for mixture of shapes. So far, we have the following shapes: "spheres" and
+            "random_needles" (i.e. randomly-oriented elongated ellipsoidal inclusions).
+            If the argument is a dict, the keys are the shapes and the values are the mixing ratio.
+            If it is a list, the mixing_ratio argument is required.
+        :param brine_mixing_ratio: The mixing ratio of the shapes. This is only relevant when inclusion_shape is a list/tuple.
+            Mixing ratio must be a sequence with length len(inclusion_shape)-1.
+            The mixing ratio of the last shapes is deduced as the sum of the ratios must equal to 1.
         :param ice_permittivity_model: pure ice permittivity formulation (default is ice_permittivity_matzler87)
         :param brine_permittivity_model: brine permittivity formulation (default is brine_permittivity_stogryn85)
     """
@@ -74,6 +78,6 @@ def saline_ice_permittivity_pvs_mixing(frequency, temperature, brine_volume_frac
     brine_permittivity = brine_permittivity_model(frequency, temperature)
 
     return polder_van_santen(brine_volume_fraction,
-                            e0=pure_ice_permittivity,
-                            eps=brine_permittivity,
-                            inclusion_shape=brine_inclusion_shape, mixing_ratio=brine_mixing_ratio)
+                             e0=pure_ice_permittivity,
+                             eps=brine_permittivity,
+                             inclusion_shape=brine_inclusion_shape, mixing_ratio=brine_mixing_ratio)

smrt/substrate/soil_wegmuller.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 
-"""Implement the empirical soil model presented in Wegmuller and Maetzler 1999. It is often used in microwave radiometry. It is 
-not suitable for the active mode.
+"""Implement the empirical soil model presented in Wegmuller and Maetzler 1999. 
+It is often used in microwave radiometry. It is not suitable for the active mode.
 
 parameters: roughness_rms