Update docs and doc strings

Author: cbegeman

docs/developers_guide/framework/model.md

@@ -20,7 +20,9 @@ method,  you can set number of tasks, threads, etc. determined from the
 `openmp_threads` attributes.  These resources need to be set at construction or
 in the  {ref}`dev-step-setup` method (i.e. before calling {ref}`dev-step-run`) 
 so that  the polaris framework  can ensure that the required resources are 
-available.
+available. If the graph partition file has been constructed prior to the ocean
+model step, the path to the graph file should be provided in the
+`graph_target` argument to {py:meth}`polaris.ocean.OceanModelStep.__init__()`.
 
 (dev-model-yaml-namelists-and-streams)=
 

docs/developers_guide/ocean/api.md

@@ -215,6 +215,7 @@
 
    init.Init
    init.Init.run
+   init.Init.setup
 
    viz.Viz
    viz.Viz.run

docs/developers_guide/organization/steps.md

@@ -244,7 +244,6 @@ class SetupMesh(Step):
             self.add_input_file(filename='mpas_grid.nc',
                                 target='dome_varres_grid.nc', database='')
 
-        self.add_output_file(filename='graph.info')
         self.add_output_file(filename='landice_grid.nc')
 ```
 
@@ -366,8 +365,6 @@ class Forward(OceanModelStep):
 
         self.add_input_file(filename='initial_state.nc',
                             target='../../init/initial_state.nc')
-        self.add_input_file(filename='graph.info',
-                            target='../../init/culled_graph.info')
 
         self.add_yaml_file('polaris.ocean.tasks.baroclinic_channel',
                            'forward.yaml')
@@ -803,9 +800,6 @@ def __init__(self, component, mesh, init):
     self.add_input_file(
         filename='forcing_data.nc',
         work_dir_target=f'{init.path}/init/init_mode_forcing_data.nc')
-    self.add_input_file(
-        filename='graph.info',
-        work_dir_target=f'{mesh_path}/culled_graph.info')
 ```
 
 (dev-step-input-polaris)=

docs/tutorials/dev_add_test_group.md

@@ -1024,8 +1024,7 @@ class Init(Step):
 
         self.resolution = resolution
 
-        for file in ['base_mesh.nc', 'culled_mesh.nc', 'culled_graph.info',
-                     'initial_state.nc']:
+        for file in ['base_mesh.nc', 'culled_mesh.nc', 'initial_state.nc']:
             self.add_output_file(file)
 ```
 
@@ -1286,8 +1285,6 @@ class Forward(OceanModelStep):
 
         self.add_input_file(filename='initial_state.nc',
                             target='../init/initial_state.nc')
-        self.add_input_file(filename='graph.info',
-                            target='../init/culled_graph.info')
 
         self.add_output_file(filename='output.nc')
 ```

polaris/ocean/convergence/forward.py

@@ -50,6 +50,10 @@ def __init__(self, component, name, subdir, resolution, mesh, init,
             A nested dictionary of options and value for each ``config_model``
             to replace model config options with new values
 
+        graph_target : str, optional
+            The graph file name (relative to the base work directory).
+            If none, it will be created.
+
         output_filename : str, optional
             The output file that will be written out at the end of the forward
             run

polaris/ocean/model/ocean_model_step.py

@@ -84,7 +84,8 @@ def __init__(self, component, name, subdir=None, indir=None, ntasks=None,
             option of the ``[executables]`` config section.
 
         graph_target : str, optional
-            The name of the graph file to partition
+            The graph file name (relative to the base work directory).
+            If none, it will be created.
         """
         if graph_target is None:
             self.make_graph = True

polaris/ocean/tasks/baroclinic_channel/forward.py

@@ -65,6 +65,10 @@ def __init__(self, component, resolution, name='forward', subdir=None,
 
         run_time_steps : int, optional
             Number of time steps to run for
+
+        graph_target : str, optional
+            The graph file name (relative to the base work directory).
+            If none, it will be created.
         """
         self.resolution = resolution
         self.run_time_steps = run_time_steps

polaris/ocean/tasks/baroclinic_channel/restart/restart_step.py

@@ -24,6 +24,9 @@ def __init__(self, component, resolution, name, indir, init):
 
         indir : str
             the directory the step is in, to which ``name`` will be appended
+
+        init: polaris.ocean.tasks.baroclinic_channel.init.Init
+            the initial state step
         """
         self.resolution = resolution
         super().__init__(component=component, name=name, indir=indir, ntasks=4,

polaris/ocean/tasks/internal_wave/forward.py

@@ -28,7 +28,7 @@ def __init__(self, component, init, name='forward', subdir=None,
         name : str
             the name of the task
 
-        init : polaris.Step
+        init : polaris.ocean.tasks.internal_wave.init.Init
             the initial state step
 
         subdir : str, optional

polaris/ocean/tasks/internal_wave/rpe/__init__.py

@@ -13,6 +13,9 @@ class Rpe(Task):
     ----------
     resolution : float
         The resolution of the test case in km
+
+    init : polaris.ocean.tasks.baroclinic_channel.init.Init
+        A shared step for creating the initial state
     """
 
     def __init__(self, component, indir, init, config, vadv_method='standard'):