Fix the word 'brief' in README; add some basic type annotations to the tests

Ignore .vscode settings directory

Author: r-barnes

.gitignore

@@ -99,6 +99,9 @@ target/
 # SublimeText docs
 *.sublime-*
 
+# VSCode settings directory
+.vscode/
+
 # temp folder
 temp/
 

README.rst

@@ -10,13 +10,13 @@ pyDeltaRCM
 
 .. image:: https://github.com/DeltaRCM/pyDeltaRCM/actions/workflows/build.yml/badge.svg
     :target: https://github.com/DeltaRCM/pyDeltaRCM/actions
-    
+
 .. image:: https://codecov.io/gh/DeltaRCM/pyDeltaRCM/branch/develop/graph/badge.svg
   :target: https://codecov.io/gh/DeltaRCM/pyDeltaRCM
 
 .. image:: https://app.codacy.com/project/badge/Grade/1c137d0227914741a9ba09f0b00a49a7
-    :target: https://www.codacy.com/gh/DeltaRCM/pyDeltaRCM?utm_source=github.com&utm_medium=referral&utm_content=DeltaRCM/pyDeltaRCM&utm_campaign=Badge_Grade    
-    
+    :target: https://www.codacy.com/gh/DeltaRCM/pyDeltaRCM?utm_source=github.com&utm_medium=referral&utm_content=DeltaRCM/pyDeltaRCM&utm_campaign=Badge_Grade
+
 
 
 
@@ -25,7 +25,7 @@ pyDeltaRCM
 
 
 .. figure:: https://deltarcm.org/pyDeltaRCM/_images/cover.png
-    
+
     Weighted random walks for 20 water parcels, in a *pyDeltaRCM* model run with default parameters.
 
 
@@ -54,7 +54,7 @@ Executing the model
 
 We recommend you check out our `pyDeltaRCM in 10 minutes tutorial <https://deltarcm.org/pyDeltaRCM/guides/10min.html>`_, which is part of our documentation.
 
-Beyond that breif tutorial, we have a comprehensive `User Documentation <https://deltarcm.org/pyDeltaRCM/index.html#user-documentation>`_ and `Developer Documentation <https://deltarcm.org/pyDeltaRCM/index.html#developer-documentation>`_ to check out.
+Beyond that brief tutorial, we have a comprehensive `User Documentation <https://deltarcm.org/pyDeltaRCM/index.html#user-documentation>`_ and `Developer Documentation <https://deltarcm.org/pyDeltaRCM/index.html#developer-documentation>`_ to check out.
 
 
 Additional notes

pyDeltaRCM/_version.py

@@ -1,5 +1,5 @@
 
-def __version__():
+def __version__() -> str:
     """
     Private version declaration, gets assigned to pyDeltaRCM.__version__
     during import

pyDeltaRCM/debug_tools.py

@@ -118,7 +118,7 @@ def show_ind(self, ind, *args, **kwargs):
         else:
             plot_ind(ind, shape=_shape, *args, **kwargs)
 
-    def show_line(self, ind, *args, multiline=False, nozeros=False, **kwargs):
+    def show_line(self, ind, *args, multiline: bool = False, nozeros: bool = False, **kwargs):
         """Show line within the model domain.
 
         Show the location of lines (a series of connected indices) within the
@@ -200,7 +200,7 @@ def show_line(self, ind, *args, multiline=False, nozeros=False, **kwargs):
         return lines
 
 
-def plot_domain(attr, ax=None, grid=True, block=False, label=None, **kwargs):
+def plot_domain(attr, ax=None, grid: bool = True, block: bool = False, label=None, **kwargs):
     """Plot the model domain.
 
     Public function to plot *any* 2d grid with helper display utils.

pyDeltaRCM/init_tools.py

@@ -23,7 +23,7 @@
 
 class init_tools(abc.ABC):
 
-    def init_output_infrastructure(self):
+    def init_output_infrastructure(self) -> None:
         """Initialize the output infrastructure (folder and save lists).
 
         This method is the first called in the initialization of the
@@ -42,7 +42,7 @@ def init_output_infrastructure(self):
         self._save_var_list = dict()  # dict of variables to save
         self._save_var_list['meta'] = dict()  # set up meta dict
 
-    def init_logger(self):
+    def init_logger(self) -> None:
         """Initialize a logger.
 
         The logger is initialized regardless of the value of ``self.verbose``.
@@ -73,7 +73,7 @@ def init_logger(self):
         self.log_info('Platform: {}'.format(platform.platform()),
                       verbosity=0)  # log the os
 
-    def import_files(self, kwargs_dict={}):
+    def import_files(self, kwargs_dict={}) -> None:
         """Import the input files.
 
         This method handles the parsing and validation of any options supplied
@@ -181,7 +181,7 @@ def import_files(self, kwargs_dict={}):
         else:
             self._netcdf_coords = ('time', 'x', 'y')
 
-    def process_input_to_model(self):
+    def process_input_to_model(self) -> None:
         """Process input file to model variables.
 
         Loop through the items specified in the model configuration and apply
@@ -210,7 +210,7 @@ def process_input_to_model(self):
                     var=k, val=v)
                 self.log_info(_msg, verbosity=0)
 
-    def determine_random_seed(self):
+    def determine_random_seed(self) -> None:
         """Set the random seed if given.
 
         If a random seed is specified, set the seed to this value.
@@ -227,7 +227,7 @@ def determine_random_seed(self):
         _msg = 'Random seed is: %s ' % str(self._seed)
         self.log_info(_msg, verbosity=0)
 
-    def create_other_variables(self):
+    def create_other_variables(self) -> None:
         """Model implementation variables.
 
         Creates variables for model implementation, from specified boundary
@@ -282,7 +282,7 @@ def create_other_variables(self):
 
         self._is_finalized = False
 
-    def set_constants(self):
+    def set_constants(self) -> None:
         """Set the model constants.
 
         Configure constants, including coordinates and distances, as well as
@@ -342,7 +342,7 @@ def set_constants(self):
                                  [1, 0, 1],
                                  [1, 1, 1]]).astype(np.int64)
 
-    def create_boundary_conditions(self):
+    def create_boundary_conditions(self) -> None:
         """Create model boundary conditions
 
         This method is run during model initialization to determine the
@@ -415,7 +415,7 @@ def create_boundary_conditions(self):
         self.diffusion_multiplier = (self._dt / self.N_crossdiff * self._alpha
                                      * 0.5 / self._dx**2)
 
-    def create_domain(self):
+    def create_domain(self) -> None:
         """Create the model domain.
 
         This method initializes the model domain, including coordinate arrays,
@@ -521,7 +521,7 @@ def create_domain(self):
         self.inlet = np.array(np.unique(np.where(self.cell_type == 1)[1]))
         self.eta[:] = self.stage - self.depth
 
-    def init_sediment_routers(self):
+    def init_sediment_routers(self) -> None:
         """Initialize the sediment router object here.
 
         These are preinitialized because the "boxing" for jitted functions is
@@ -555,7 +555,7 @@ def init_sediment_routers(self):
                                         self._beta, self.stepmax,
                                         self.theta_sand)
 
-    def init_output_file(self):
+    def init_output_file(self) -> None:
         """Creates a netCDF file to store output grids.
 
         Fills with default variables.
@@ -679,7 +679,7 @@ def _create_meta_variable(varname, varvalue, varunits,
             _msg = 'Output netCDF file created'
             self.log_info(_msg, verbosity=2)
 
-    def init_subsidence(self):
+    def init_subsidence(self) -> None:
         """Initialize subsidence pattern.
 
         Initializes patterns of subsidence if toggle_subsidence is True
@@ -702,7 +702,7 @@ def init_subsidence(self):
 
             self.sigma = self.subsidence_mask * self._subsidence_rate * self.dt
 
-    def init_metadata_list(self):
+    def init_metadata_list(self) -> None:
         """Populate the list of metadata information.
 
         Sets up the dictionary object for the standard metadata.

pyDeltaRCM/iteration_tools.py

@@ -23,7 +23,7 @@ class iteration_tools(abc.ABC):
     these operations largely occur when saving and updating the model.
     """
 
-    def solve_water_and_sediment_timestep(self):
+    def solve_water_and_sediment_timestep(self) -> None:
         """Run water and sediment operations for one timestep.
 
         The first operation called by :meth:`update`, this method iterates the
@@ -48,7 +48,7 @@ def solve_water_and_sediment_timestep(self):
         self.route_sediment()
         self.hook_after_route_sediment()
 
-    def run_one_timestep(self):
+    def run_one_timestep(self) -> None:
         """Deprecated, since v1.3.1. Use :obj:`solve_water_and_sediment_timestep`."""
         _msg = ('`run_one_timestep` and `hook_run_one_timestep` are '
                 'deprecated and have been replaced with '
@@ -87,7 +87,7 @@ def apply_subsidence(self):
 
                 self.eta[:] = self.eta - self.sigma
 
-    def finalize_timestep(self):
+    def finalize_timestep(self) -> None:
         """Finalize timestep.
 
         Clean up after sediment routing. This includes a correction for
@@ -117,7 +117,7 @@ def finalize_timestep(self):
 
         self.H_SL = self._H_SL + self._SLR * self._dt
 
-    def log_info(self, message, verbosity=0):
+    def log_info(self, message: str, verbosity: int = 0) -> None:
         """Log message dependent on verbosity settings.
 
         Parameters
@@ -132,7 +132,7 @@ def log_info(self, message, verbosity=0):
         if self._verbose >= verbosity:
             self.logger.info(message)
 
-    def log_model_time(self):
+    def log_model_time(self) -> None:
         """Log the time of the model.
 
         Reports the time to the log file, and depending on verbosity, will
@@ -144,7 +144,7 @@ def log_model_time(self):
         if self._verbose > 0:
             print(_timemsg)
 
-    def output_data(self):
+    def output_data(self) -> None:
         """Output grids and figures if needed.
 
         """
@@ -155,7 +155,7 @@ def output_data(self):
             self._save_iter += int(1)
             self._save_time_since_data = 0
 
-    def output_checkpoint(self):
+    def output_checkpoint(self) -> None:
         """Output checkpoint if needed.
 
         Save checkpoint data (including rng state) so that the model can be
@@ -186,7 +186,7 @@ def output_checkpoint(self):
 
                 self._save_time_since_checkpoint = 0
 
-    def compute_sand_frac(self):
+    def compute_sand_frac(self) -> None:
         """Compute the sand fraction as a continous updating data field.
 
         Parameters
@@ -235,7 +235,7 @@ def compute_sand_frac(self):
             self.sand_frac[whr_agg] = mixture
             self.active_layer[whr_agg] = mixture
 
-    def save_grids_and_figs(self):
+    def save_grids_and_figs(self) -> None:
         """Save grids and figures.
 
         Save grids and/or plots of specified variables (``eta``, `discharge``,
@@ -330,7 +330,7 @@ def save_grids_and_figs(self):
 
             self.output_netcdf.sync()
 
-    def make_figure(self, var, timestep):
+    def make_figure(self, var, timestep) -> None:
         """Create a figure.
 
         Parameters
@@ -362,7 +362,7 @@ def make_figure(self, var, timestep):
         return fig
 
     def save_figure(self, fig, directory, filename_root,
-                    timestep, ext='.png', close=True):
+                    timestep, ext: str = '.png', close: bool = True) -> None:
         """Save a figure.
 
         Parameters
@@ -396,7 +396,7 @@ def save_figure(self, fig, directory, filename_root,
         if close:
             plt.close()
 
-    def save_grids(self, var_name, var, ts):
+    def save_grids(self, var_name: str, var: np.ndarray, ts: int) -> None:
         """Save a grid into an existing netCDF file.
 
         File should already be open (by :meth:`init_output_grid`) as
@@ -427,7 +427,7 @@ def save_grids(self, var_name, var, ts):
             self.logger.error(_msg)
             raise Exception(e)
 
-    def save_the_checkpoint(self):
+    def save_the_checkpoint(self) -> None:
         """Save checkpoint files.
 
         Saves the grids to a .npz file so that the model can be