add verbosity and random seed options to the yaml parser, change the …

…behavior of the verbose flag to be an integer, default is 0, silent, 1 is some output on each timestep, 2 is lots of output all over the place

pyDeltaRCM/default.yml

@@ -7,6 +7,12 @@ case_prefix:
 out_dir:
   type: 'str'
   default: 'deltaRCM_Output'
+verbose:
+  type: 'int'
+  default: 0
+seed:
+  type: 'int'
+  default: -1
 Length:
   type: 'float'
   default: 1000.

pyDeltaRCM/deltaRCM_driver.py

@@ -8,11 +8,7 @@
 
 class pyDeltaRCM(Tools):
 
-    #############################################
-    ################## __init__ #################
-    #############################################
-
-    def __init__(self, input_file = None):
+    def __init__(self, input_file=None):
         """Creates an instance of the pyDeltaRCM model.
 
         This method handles setting up the run, including parsing input files,
@@ -33,7 +29,6 @@ def __init__(self, input_file = None):
         self._time = 0.
         self._time_step = 1.
 
-        self.verbose = False
         self.input_file = input_file
         self._file_dir = os.path.realpath(os.path.dirname(__file__))
         self.default_file = os.path.join(self._file_dir, 'default.yml')
@@ -71,7 +66,7 @@ def finalize(self):
 
         try:
             self.output_netcdf.close()
-            if self.verbose:
+            if self.verbose >= 1:
                 print('Closed output netcdf file.')
         except Exception:
             pass

pyDeltaRCM/deltaRCM_tools.py

@@ -23,8 +23,6 @@
 from .water_tools import water_tools
 from .init_tools import init_tools
 
-np.random.seed(0)
-
 
 class Tools(sed_tools, water_tools, init_tools, object):
 
@@ -35,9 +33,9 @@ def run_one_timestep(self):
 
         timestep = self._time
 
-        if self.verbose:
+        if self.verbose > 0:
             print('-' * 20)
-            print('Time = ' + str(self._time))
+            print('Timestep: ' + str(self._time))
 
         for iteration in range(self.itermax):
 
@@ -100,7 +98,7 @@ def record_stratigraphy(self):
             if self.strata_eta.shape[1] <= timestep:
                 self.expand_stratigraphy()
 
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('Storing stratigraphy data')
 
             # ------------------ sand frac ------------------
@@ -161,7 +159,7 @@ def apply_subsidence(self):
             timestep = self._time
 
             if self.start_subsidence <= timestep:
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Applying subsidence')
                 self.eta[:] = self.eta - self.sigma
 
@@ -223,27 +221,27 @@ def output_data(self):
 
             # ------------------ grids ------------------
             if self.save_eta_grids:
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Saving grid: eta')
                 self.save_grids('eta', self.eta, shape[0])
 
             if self.save_depth_grids:
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Saving grid: depth')
                 self.save_grids('depth', self.depth, shape[0])
 
             if self.save_stage_grids:
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Saving grid: stage')
                 self.save_grids('stage', self.stage, shape[0])
 
             if self.save_discharge_grids:
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Saving grid: discharge')
                 self.save_grids('discharge', self.qw, shape[0])
 
             if self.save_velocity_grids:
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Saving grid: velocity')
                 self.save_grids('velocity', self.uw, shape[0])
 
@@ -254,7 +252,7 @@ def output_strata(self):
 
         if self.save_strata:
 
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('\nSaving final stratigraphy to netCDF file')
 
             self.strata_eta = self.strata_eta[:, :self.strata_counter]
@@ -295,7 +293,7 @@ def output_strata(self):
 
                 self.output_netcdf.variables['strata_depth'][i, :, :] = sz
 
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('Stratigraphy data saved.')
 
     def save_figure(self, path, ext='png', close=True):
@@ -318,7 +316,7 @@ def save_figure(self, path, ext='png', close=True):
             directory = '.'
 
         if not os.path.exists(directory):
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('Creating output directory')
             os.makedirs(directory)
 

pyDeltaRCM/init_tools.py

@@ -29,7 +29,7 @@ class init_tools(object):
 
     def init_logger(self):
 
-        if self.verbose:
+        if self.verbose >= 1:
 
             self.logger = logging.getLogger("driver")
             self.logger.setLevel(logging.INFO)
@@ -85,6 +85,9 @@ def import_files(self):
         for k, v in list(input_file_vars.items()):
             setattr(self, k, v)
 
+        if self.seed >= 0:
+            np.random.seed(self.seed)
+
     def set_constants(self):
 
         self.g = 9.81   # (gravitation const.)
@@ -128,6 +131,15 @@ def set_constants(self):
                                  [1, 1, 1]])
 
     def create_other_variables(self):
+        """Model implementation variables.
+
+        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``.
+        """
 
         self.init_Np_water = self.Np_water
         self.init_Np_sed = self.Np_sed
@@ -323,21 +335,21 @@ def init_output_grids(self):
                 self.save_velocity_grids or
                 self.save_strata):
 
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('Generating netCDF file for output grids...')
 
             directory = self.prefix
             filename = 'pyDeltaRCM_output.nc'
 
             if not os.path.exists(directory):
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('Creating output directory')
                 os.makedirs(directory)
 
             file_path = os.path.join(directory, filename)
 
             if os.path.exists(file_path):
-                if self.verbose:
+                if self.verbose >= 2:
                     self.logger.info('*** Replaced existing netCDF file ***')
                 os.remove(file_path)
 
@@ -396,7 +408,7 @@ def init_output_grids(self):
                                                              ('total_time', 'length', 'width'))
                 velocity.units = 'meters per second'
 
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('Output netCDF file created.')
 
     def init_subsidence(self):

pyDeltaRCM/sed_tools.py

@@ -22,6 +22,7 @@
 
 # tools for sediment routing algorithms and deposition/erosion
 
+
 class sed_tools(shared_tools):
 
     def sed_route(self):

pyDeltaRCM/water_tools.py

@@ -489,7 +489,7 @@ def check_size_of_indices_matrix(self, it):
             self.iter for all further timesteps
             """
 
-            if self.verbose:
+            if self.verbose >= 2:
                 self.logger.info('Increasing size of self.indices')
 
             indices_blank = np.zeros(

tests/test.yaml

@@ -3,6 +3,7 @@ case_prefix: ''
 out_dir: test
 Length: 10.0
 Width: 10.0
+seed: 0
 dx: 1.0
 L0_meters: 1.0
 S0: 0.0002

tests/test_init_tools.py

@@ -16,6 +16,14 @@
 # now that it is initiated can access the init_tools via the inherited object
 # delta.**init_tools_function**
 
+# Tests for attrs set during yaml parsing
+def test_set_verbose():
+    assert delta.verbose == 0
+
+
+def test_set_seed():
+    assert delta.seed == 0
+
 
 # Tests for all of the constants
 delta.set_constants()