Sandsuet output

docs/source/examples/custom_saving.rst

@@ -17,11 +17,11 @@ For example, ``self._save_fig_list['active_layer'] = ['active_layer']`` will pro
 When adding variables or metadata to be initialized and subsequently saved in the output netCDF, the key-value pair relationship is as follows.
 The key added to ``self._save_var_list`` is the name of the variable as it will be recorded in the netCDF file, this *does not* have to correspond to the name of an attribute in the model.
 To add a variable to the metadata, a key must be added to ``self._save_var_list['meta']``.
-The expected value for a given key is a list containing strings indicating the model attribute to be saved, its units, the variable type, and lastly the variable dimensions (e.g., ``['active_layer', 'fraction', 'f4', ('time', 'x', 'y')]`` for the active layer).
+The expected value for a given key is a list containing strings indicating the model attribute to be saved, its units, the variable type, and lastly the variable dimensions (e.g., ``['active_layer', 'fraction', 'f4', ('seconds', 'x', 'y')]`` for the active layer).
 
 .. important::
 
-    The dimensions of the custom variable being specified must match *exactly* with one of the three standard dimensions: `x`, `y`, `time`.
+    The dimensions of the custom variable being specified must match *exactly* with one of the three standard dimensions: `x`, `y`, `seconds`.
     Use of an invalid dimension will result in an error.
 
 An example of using the hook and creating a model subclass to customize the figures, gridded variables, and metadata being saved is provided below.
@@ -48,14 +48,19 @@ An example of using the hook and creating a model subclass to customize the figu
     ...         self._save_fig_list['active_layer'] = ['active_layer']
     ...
     ...         # save the active layer grid each save_dt w/ a short name
-    ...         self._save_var_list['actlay'] = ['active_layer', 'fraction',
-    ...                                          'f4', ('time',
-    ...                                                 'x', 'y')]
+    ...         self._save_var_list['actlay'] = [
+    ...             'active_layer', 'fraction',
+    ...             'f4', ('seconds', 'x', 'y'),
+    ...             'channel_bottom__sediment__active_layer'
+    ...             ]
     ...
     ...         # save number of water parcels w/ a long name
-    ...         self._save_var_list['meta']['water_parcels'] = ['Np_water',
-    ...                                                         'parcels',
-    ...                                                         'i8', ()]
+    ...         self._save_var_list['meta']['water_parcels'] = [
+    ...             'Np_water',
+    ...             'parcels',
+    ...             'i8', (),
+    ...             'model_water__number_parcels'
+    ...             ]
 
 Next, we instantiate the model class.
 
@@ -83,4 +88,4 @@ For simplicity we will just check that the appropriate parameters were added to
     {'active_layer': ['active_layer']}
 
     >>> print(mdl._save_var_list)
-    {'meta': {'water_parcels': ['Np_water', 'parcels', 'i8', ()]}, 'actlay': ['active_layer', 'fraction', 'f4', ('time', 'x', 'y')]}
+    {'meta': {'water_parcels': ['Np_water', 'parcels', 'i8', (), 'model_water__number_parcels']}, 'actlay': ['active_layer', 'fraction', 'f4', ('seconds', 'x', 'y'), 'channel_bottom__sediment__active_layer']}

docs/source/info/outputfile.rst

@@ -10,30 +10,35 @@ Gridded Variables
 
 In any given run, the saving parameters "save_<var>_grids" control whether or
 not that 2-D grid variable (e.g. velocity) is saved to the netCDF4 file. In
-the netCDF4 file, a 3-D array with the dimensions `time` :math:`\times`
+the netCDF4 file, a 3-D array with the dimensions `seconds` :math:`\times`
 `x` :math:`\times` `y` is created for each 2-D grid variable that is set to
 be saved. Note that `x` is the *downstream* coordinate, rather than the
 Cartesian `x` when displaying the grid. The appropriate units for all
 variables are stored: for example "meters per second" for the *velocity*
-grid.
+grid. All variables include a description via the `long_name` attribute.
 
-.. note::
+.. important::
 
-   The format of the output netCDF file coordinate changed in `v2.1.0`. The
-   old format is documented
-   in :attr:`~pyDeltaRCM.model.DeltaModel.legacy_netcdf`, and that input
-   parameter `legacy_netcdf` can be used to create on output netcdf file with
-   the old coordinate configuration.
+   The format of the output netCDF file coordinates changed in `v2.2.0`. The
+   old format (up to v2.1.9) is documented
+   in :attr:`~pyDeltaRCM.model.DeltaModel.legacy_netcdf`, and the input
+   parameter `legacy_netcdf` can be used to create an output netcdf file with
+   the old coordinate configuration. The output format for pyDeltaRCM v2.1.0
+   and earlier is deprecated and has been removed. Changing to the new output
+   format should be a small change for most users, with only the name of the
+   temporal dimension and the metadata subgroup changing in the new output.
 
 
 Grid Coordinates
 ================
 
-Grid coordinates are specified in the variables `time`, `x`, and `y` in the output netCDF4 file.
-These arrays are 1D arrays, which specify the location of each cell in the domain in *dimensional* coordinates (e.g., meters).
-In the downstream direction,  the distance of each cell from the inlet boundary is specified in `x` in meters.
-Similarly, the cross-domain distance is specified in `y` in meters.
-Lastly, the `time` variable is stored as a 1D array with model `time` in seconds.
+Grid coordinates are specified in the variables `seconds`, `x`, and `y` in the
+output netCDF4 file. These arrays are 1D arrays, which specify the location
+of each cell in the domain in *dimensional* coordinates (e.g., meters). In
+the downstream direction,  the distance of each cell from the inlet boundary
+is specified in `x` in meters. Similarly, the cross-domain distance is
+specified in `y` in meters. Lastly, the `seconds` variable is stored as a 1D
+array recording model elapsed time in seconds.
 
 
 Model Metadata
@@ -53,6 +58,7 @@ saved as metadata are the following:
 - Sediment concentration: `C0_percent`
 - Characteristic Velocity: `u0`
 - If subsidence is enabled:
+
   - Subsidence start time: `start_subsidence`
   - Subsidence rate: `sigma`
 
@@ -66,7 +72,7 @@ library. These libraries range from the
 to higher-level libraries such as
 `xarray <https://github.com/pydata/xarray>`_. For deltas, and specifically
 *pyDeltaRCM*, there is also a package under development called
-`DeltaMetrics <https://github.com/DeltaRCM/DeltaMetrics>`_,
+`sandplover <https://github.com/sandpiper-toolchain/sandplover>`_,
 that is being designed to help post-process and analyze *pyDeltaRCM* outputs.
 
 

pyDeltaRCM/_version.py

@@ -3,4 +3,4 @@ def __version__() -> str:
     Private version declaration, gets assigned to pyDeltaRCM.__version__
     during import
     """
-    return "2.1.9"
+    return "2.2.0"

pyDeltaRCM/hook_tools.py

@@ -237,7 +237,7 @@ def hook_init_output_file(self) -> None:
         .. note::
 
             For a vector of time-varying metadata, the dimension
-            should be specified as ('total_time').
+            should be specified as ('time').
 
         Expected format for time varying grid entries as keys within the
         `self._save_var_list` dictionary: