Improve "code quality"

.bandit.yml

@@ -0,0 +1,2 @@
+exclude_dirs:
+	tests/**

README.rst

@@ -8,6 +8,8 @@ pyDeltaRCM_WMT
 .. image:: https://coveralls.io/repos/github/DeltaRCM/pyDeltaRCM_WMT/badge.svg?branch=develop
     :target: https://coveralls.io/github/DeltaRCM/pyDeltaRCM_WMT?branch=develop
 
+.. image:: https://app.codacy.com/project/badge/Grade/1c137d0227914741a9ba09f0b00a49a7
+    :target: https://www.codacy.com/gh/DeltaRCM/pyDeltaRCM_WMT?utm_source=github.com&utm_medium=referral&utm_content=DeltaRCM/pyDeltaRCM_WMT&utm_campaign=Badge_Grade
 
 pyDeltaRCM is the Python version of the `Matlab deltaRCM <https://csdms.colorado.edu/wiki/Model:DeltaRCM>`_ model by Man Liang. 
 The pyDeltaRCM scripts in this repository can be run as a stand-alone model following the instructions below.

pyDeltaRCM/deltaRCM_tools.py

@@ -1,24 +1,12 @@
 #! /usr/bin/env python
 
-import sys
 import os
-import re
-import string
-import logging
-import time
 import warnings
 
-from math import floor, sqrt, pi
 import numpy as np
-from random import shuffle
-
-import matplotlib
-from matplotlib import pyplot as plt
+import matplotlib.pyplot as plt
 
 from scipy.sparse import lil_matrix, csc_matrix, hstack
-from scipy import ndimage
-
-from netCDF4 import Dataset
 
 from .sed_tools import sed_tools
 from .water_tools import water_tools
@@ -46,7 +34,6 @@ def run_one_timestep(self):
         RuntimeError 
             If model has already been finalized via :meth:`finalize`.
         """
-
         timestep = self._time
 
         self.logger.info('-' * 4 + ' Timestep ' +
@@ -70,7 +57,7 @@ def run_one_timestep(self):
         self.sed_route()
 
     def finalize_timestep(self):
-        """
+        """Finalize timestep.
 
         Clean up after sediment routing. This includes a correction for
         flooded cells that are not "wet" (via :meth:`flooding_correction`).
@@ -84,7 +71,6 @@ def finalize_timestep(self):
         -------
 
         """
-
         self.flooding_correction()
         self.stage[:] = np.maximum(self.stage, self.H_SL)
         self.depth[:] = np.maximum(self.stage - self.eta, 0)
@@ -104,7 +90,6 @@ def expand_stratigraphy(self):
         -------
 
         """
-
         _msg = 'Expanding stratigraphy arrays'
         self.logger.info(_msg)
         if self.verbose >= 2:
@@ -139,7 +124,6 @@ def record_stratigraphy(self):
         -------
 
         """
-
         timestep = self._time
 
         if self.save_strata and (timestep % self.save_dt == 0):
@@ -213,7 +197,6 @@ def apply_subsidence(self):
         -------
 
         """
-
         if self.toggle_subsidence:
 
             timestep = self._time
@@ -241,7 +224,6 @@ def output_data(self):
         -------
 
         """
-
         timestep = self._time
 
         if timestep % self.save_dt == 0:
@@ -331,7 +313,6 @@ def output_strata(self):
         -------
 
         """
-
         if self.save_strata:
 
             _msg = 'Saving final stratigraphy to netCDF file'
@@ -404,7 +385,6 @@ def save_figure(self, path, ext='png', close=True):
         -------
 
         """
-
         directory = os.path.split(path)[0]
         filename = "%s.%s" % (os.path.split(path)[1], ext)
         if directory == '':
@@ -442,7 +422,6 @@ def save_grids(self, var_name, var, ts):
         -------
 
         """
-
         try:
             self.output_netcdf.variables[var_name][ts, :, :] = var
         except:

pyDeltaRCM/init_tools.py

@@ -1,27 +1,16 @@
 
-import sys
 import os
-import re
-import string
 import logging
-# import time
 import warnings
 
 from math import floor, sqrt, pi
 import numpy as np
-from random import shuffle
 
-import matplotlib
-from matplotlib import pyplot as plt
-
-from scipy.sparse import lil_matrix, csc_matrix, hstack
+from scipy.sparse import lil_matrix
 from scipy import ndimage
 
 from netCDF4 import Dataset
 import time as time_lib
-from scipy.sparse import lil_matrix, csc_matrix, hstack
-import logging
-# import time
 import yaml
 
 from . import shared_tools
@@ -44,13 +33,10 @@ def init_output_infrastructure(self):
 
     def init_logger(self):
         """Initialize a logger.
-
         The logger is initialized regardless of the value of ``self.verbose``.
         The level of information printed to the log depends on the verbosity
         setting. 
-
         """
-
         self.logger = logging.getLogger('driver')
         self.logger.setLevel(logging.INFO)
 
@@ -180,11 +166,10 @@ def create_other_variables(self):
         Creates variables for model implementation, from specified boundary
         condition variables. This method is run during initial model
         instantition, but it is also run any time an inlet flow condition
-        variable is changed, including ``channel_flow_velocity``,
-        ``channel_width``, ``channel_flow_depth``, and
-        ``influx_sediment_concentration``.
+        variable is changed, including `channel_flow_velocity`,
+        `channel_width`, `channel_flow_depth`, and
+        `influx_sediment_concentration`.
         """
-
         self.init_Np_water = self.Np_water
         self.init_Np_sed = self.Np_sed
 
@@ -258,19 +243,16 @@ def create_domain(self):
         """
         Creates the model domain
         """
-
         self.logger.info('Creating model domain')
 
         # ---- empty arrays ----
         self.x, self.y = np.meshgrid(
             np.arange(0, self.W), np.arange(0, self.L))
 
         self.cell_type = np.zeros((self.L, self.W), dtype=np.int)
-
         self.eta = np.zeros((self.L, self.W)).astype(np.float32)
         self.stage = np.zeros((self.L, self.W)).astype(np.float32)
         self.depth = np.zeros((self.L, self.W)).astype(np.float32)
-
         self.qx = np.zeros((self.L, self.W))
         self.qy = np.zeros((self.L, self.W))
         self.qxn = np.zeros((self.L, self.W))
@@ -279,11 +261,9 @@ def create_domain(self):
         self.ux = np.zeros((self.L, self.W))
         self.uy = np.zeros((self.L, self.W))
         self.uw = np.zeros((self.L, self.W))
-
         self.qs = np.zeros((self.L, self.W))
         self.Vp_dep_sand = np.zeros((self.L, self.W))
         self.Vp_dep_mud = np.zeros((self.L, self.W))
-
         self.free_surf_flag = np.zeros((self.Np_water,), dtype=np.int)
         self.looped = np.zeros((self.Np_water,))
         self.indices = np.zeros((self.Np_water, self.size_indices),
@@ -342,8 +322,7 @@ def create_domain(self):
         self.clim_eta = (-self.h0 - 1, 0.05)
 
     def init_stratigraphy(self):
-        """Creates sparse array to store stratigraphy data.
-        """
+        """Creates sparse array to store stratigraphy data."""
         if self.save_strata:
 
             self.strata_counter = 0
@@ -365,7 +344,6 @@ def init_output_grids(self):
         .. warning:: Overwrites an existing netcdf file with the same name.
 
         """
-
         if (self.save_eta_grids or
                 self.save_depth_grids or
                 self.save_stage_grids or
@@ -456,7 +434,6 @@ def init_subsidence(self):
 
         Modify the equations for self.subsidence_mask and self.sigma as desired
         """
-
         if self.toggle_subsidence:
 
             R1 = 0.3 * self.L

pyDeltaRCM/model.py

@@ -24,9 +24,7 @@ class DeltaModel(Tools):
     Finally, after all ``update`` steps are complete, the model should be
     finalized (:meth:`finalize`), such that files and data are appropriately
     closed and written to disk.
-
     """
-
     def __init__(self, input_file=None):
         """Creates an instance of the pyDeltaRCM model.
 
@@ -47,7 +45,6 @@ def __init__(self, input_file=None):
         :doc:`../../guides/userguide`.
 
         """
-
         self._time = 0.
         self._time_step = 1.
 
@@ -91,7 +88,6 @@ def update(self):
         -------
 
         """
-
         self.run_one_timestep()
 
         self.apply_subsidence()
@@ -116,9 +112,7 @@ def finalize(self):
         -------
 
         """
-
         self.logger.info('Finalize model run')
-
         self.output_strata()
 
         try:
@@ -141,7 +135,6 @@ def time_step(self):
         UserWarning
             If a very small timestep is configured.
         """
-
         return self._time_step
 
     @time_step.setter
@@ -160,7 +153,7 @@ def time_step(self, new_dt):
 
     @property
     def channel_flow_velocity(self):
-        """ Get channel flow velocity """
+        """Get channel flow velocity."""
         return self.u0
 
     @channel_flow_velocity.setter
@@ -170,7 +163,7 @@ def channel_flow_velocity(self, new_u0):
 
     @property
     def channel_width(self):
-        """ Get channel width """
+        """Get channel width."""
         return self.N0_meters
 
     @channel_width.setter
@@ -180,7 +173,7 @@ def channel_width(self, new_N0):
 
     @property
     def channel_flow_depth(self):
-        """ Get channel flow depth """
+        """Get channel flow depth."""
         return self.h0
 
     @channel_flow_depth.setter
@@ -190,7 +183,7 @@ def channel_flow_depth(self, new_d):
 
     @property
     def sea_surface_mean_elevation(self):
-        """ Get sea surface mean elevation """
+        """Get sea surface mean elevation."""
         return self.H_SL
 
     @sea_surface_mean_elevation.setter
@@ -199,17 +192,16 @@ def sea_surface_mean_elevation(self, new_se):
 
     @property
     def sea_surface_elevation_change(self):
-        """ Get rate of change of sea surface elevation, per timestep"""
+        """Get rate of change of sea surface elevation, per timestep."""
         return self.SLR
 
     @sea_surface_elevation_change.setter
     def sea_surface_elevation_change(self, new_SLR):
-        """ Set rate of change of sea surface elevation, per timestep"""
         self.SLR = new_SLR
 
     @property
     def bedload_fraction(self):
-        """ Get bedload fraction """
+        """Get bedload fraction."""
         return self.f_bedload
 
     @bedload_fraction.setter
@@ -218,7 +210,7 @@ def bedload_fraction(self, new_u0):
 
     @property
     def influx_sediment_concentration(self):
-        """ Get influx sediment concentration """
+        """Get influx sediment concentration."""
         return self.C0_percent
 
     @influx_sediment_concentration.setter
@@ -228,15 +220,15 @@ def influx_sediment_concentration(self, new_u0):
 
     @property
     def sea_surface_elevation(self):
-        """ Get stage """
+        """Get stage."""
         return self.stage
 
     @property
     def water_depth(self):
-        """ Get depth """
+        """Get depth."""
         return self.depth
 
     @property
     def bed_elevation(self):
-        """ Get bed elevation """
+        """Get bed elevation."""
         return self.eta