Write Usage section

docs/installation-check.rst

@@ -9,4 +9,4 @@ and importing *pymt*:
 
 By default, no models are installed with *pymt*.
 Instructions for installing models into *pymt*
-are given in :ref:`install-a-model`.
+are given in the section :ref:`install-a-model`.

docs/installation-environment.rst

@@ -11,7 +11,7 @@ to the list of enabled conda channels on your machine:
     $ conda config --add channels conda-forge
 
 We advise installing *pymt* into a conda environment
-(see :doc:`conda-environments` section).
+(see the :doc:`conda-environments` section).
 Conda environments can easily be created and discarded.
 Create an environment for *pymt* with:
 

docs/usage.rst

@@ -2,45 +2,366 @@
 Usage
 =====
 
-.. todo::
+In this section,
+we describe the primary programmatic elements of *pymt*
+and explain how to use them to
+configure, run, and couple models.
 
-   Describe how each *pymt* method is used in running and coupling models.
-   Think of this as an expanded version of the "Basic Concepts" section
-   in the :doc:`quickstart`.
+We assume here that you have
+installed *pymt*,
+following the instructions in the :doc:`installation` guide.
+Below,
+we'll use the `CEM`_ and `Waves`_ models.
+Install them with:
 
+.. code-block:: console
 
-To use *pymt* in a project:
+    $ conda install pymt_cem
+
+
+Loading *pymt*
+--------------
+
+*pymt* is distributed as a Python `package`_.
+To use *pymt*,
+it has to be `imported`_ into a Python session.
+For example,
+the entire package can be loaded with a single import:
 
 .. code-block:: python
 
-    import pymt
+    >>> import pymt
 
-Loading a model
-+++++++++++++++
+Alternately,
+models that have been installed into *pymt*
+can be imported individually:
 
 .. code-block:: python
 
   >>> from pymt.models import Waves
-  >>> waves = Waves()
-  >>> help(Waves)
+
+Either technique is acceptable,
+but there's a slight Pythonic preference
+for loading individual models as needed.
+We'll use this technique in the remainder of this section.
+In either case,
+*pymt* must always be imported into a Python session
+before it can be used.
+
+
+.. _instantiating-a-model:
+
+
+Instantiating a model
+---------------------
+
+After importing a *pymt* model into a Python session,
+you can create an `instance`_  of it
+(also known as an `object`_):
+
+.. code-block:: python
+
+  >>> model = Waves()
+
+It is through an instance
+that we can configure, interact with, and run a model in *pymt*.
+The instance we've created here, ``model``, contains information
+(called `properties`_ or data) about the Waves model
+(e.g., its inputs and outputs, its time step, its spatial domain),
+as well as programs (called `methods`_)
+that allow access to these data.
+The sections below describe some of the data and methods
+that are associated with a model instance in *pymt*.
+
 
 Model setup
-+++++++++++
+-----------
+
+The *setup* method configures a model run.
+It's used to:
+
+* set individual model input variables,
+* generate a model configuration file for a run, and
+* make a run directory.
+
+Depending on a user's preference,
+*setup* can be invoked in different ways.
+For example,
+given a Waves instance like the one created
+in :ref:`the previous section<instantiating-a-model>`,
+a basic call to *setup* would be:
 
 .. code-block:: python
 
-  >>> from pymt.models import Waves
-  >>> waves = Waves()
-  >>> waves.setup()
+  >>> cfg_file, cfg_dir = model.setup()
+
+This creates a model configuration file with default parameters
+in a run directory in a temporary location on the filessytem.
+It returns the name of configuration file and
+the path to the run directory:
 
-  >>> waves.setup(mean_wave_height=2.)
+.. code-block:: python
+
+  >>> print(cfg_file, cfg_dir)
+  waves.txt /tmp/tmpeydq6usd
 
-Model initialization
-++++++++++++++++++++
+Note that the two outputs could also be grouped
+into a single variable; e.g.:
+
+.. code-block:: python
+
+  >>> args = model.setup()
+
+Alternately,
+the run directory can be specified.
+For example,
+to run the model in the current directory:
+
+.. code-block:: python
+
+  >>> cfg_dir = '.'
+  >>> model.setup(cfg_dir)
+
+Here,
+we didn't use the outputs from *setup*
+because the run directory has been specified,
+and the configuration file is created within it.
+
+Model inputs can also be configured with *setup*.
+Find the default values of the inputs by querying the
+*parameters* property of the model:
+
+.. code-block:: python
+
+  >>> for name, value in model.parameters:
+  ...     print(name, '=', value)
+  ...
+  run_duration = 3650
+  incoming_wave_height = 2.0
+  incoming_wave_period = 7.0
+  angle_highness_factor = 0.2
+  angle_asymmetry = 0.5
+
+Configure the model to use an incoming wave height of 3.5,
+instead of the default 2.0, meters:
+
+.. code-block:: python
+
+  >>> waves.setup(cfg_dir, incoming_wave_height=3.5)
+
+Check the *parameters* property to verify that the model inputs
+have been updated.
+
+
+Lifecycle methods
+-----------------
+
+The *initialize* and *finalize* methods
+are used to start and complete a model run.
+*Initialize* sets the initial conditions for a model,
+while *finalize* cleans up any resources
+allocated for the model run.
+
+*Initialize* requires a model configuration file.
+The run directory is an optional argument;
+if it's not provided, the current directory is assumed.
+
+Using the Waves model as an example,
+the steps to import, instantiate, set up,
+and initialize the model are:
 
 .. code-block:: python
 
   >>> from pymt.models import Waves
   >>> waves = Waves()
   >>> config_file, config_dir = waves.setup()
   >>> waves.initialize(config_file, dir=config_dir)
+
+Note that if the outputs from *setup*
+had been stored in a single variable,
+the values could be unpacked in the call to *initialize*:
+
+.. code-block:: python
+
+  >>> config = waves.setup()
+  >>> waves.initialize(*config)
+
+Further, if a model configuration file already exists,
+it can be passed directly to *initialize*,
+and the call to *setup* could be omitted.
+
+*Finalize* ends a model run.
+It takes no arguments:
+
+.. code-block:: python
+
+  >>> waves.finalize()
+
+No further operations can be performed on a model
+after it has been finalized.
+
+
+Time methods
+------------
+
+The start time, end time, and current time in a model
+are reported through a model's
+`Basic Model Interface`_
+and accessed in *pymt* through a set of three methods:
+*get_start_time*, *get_end_time*, and *get_current_time*.
+To demonstrate these methods,
+create and initialize a new instance of the Waves model:
+
+.. code-block:: python
+
+  >>> waves = Waves()
+  >>> config = waves.setup()
+  >>> waves.initialize(*config)
+
+then call these time methods with:
+
+.. code-block:: python
+
+  >>> waves.get_start_time()
+  0.0
+  >>> waves.get_end_time()
+  3650.0
+  >>> waves.get_current_time()
+  0.0
+
+Use the *time_units* property to see the
+units associated with these time values:
+
+.. code-block:: python
+
+  >>> waves.time_units
+  'd'
+
+CSDMS recommends using time unit conventions from Unidata’s `UDUNITS`_ package.
+
+Finally,
+find the model time step through the 
+*get_time_step* method:
+
+.. code-block:: python
+
+  >>> waves.get_time_step()
+  1.0
+
+
+Updating model state
+--------------------
+
+A model can be advanced through time,
+one step at a time,
+with the the *update* method.
+
+Update the instance of Waves created in the previous section
+by a single time step,
+checking the time before and after the update:
+
+.. code-block:: python
+
+  >>> waves.get_current_time()
+  0.0
+  >>> waves.update()
+  >>> waves.get_current_time()
+  1.0
+
+Although we verified that the model time has been updated,
+it would be more interesting to see model variables change.
+In the next two sections,
+we'll find what variables a model exposes,
+and how to get their values.
+
+
+Getting variable names
+----------------------
+
+What variables does a model expose for input and output,
+for exchange with other models?
+These aren't internal variables in the model source code
+(like loop counters),
+but rather variables that have `CSDMS Standard Names`_
+and are exposed through a model's `Basic Model Interface`_.
+
+The *input_var_names* and *output_var_names* properties
+list the variables exposed by a model.
+Find the variables exposed by our Waves instance:
+
+.. code-block:: python
+
+  >>> waves.input_var_names
+  ('sea_surface_water_wave__height',
+   'sea_surface_water_wave__period',
+   'sea_shoreline_wave~incoming~deepwater__ashton_et_al_approach_angle_highness_parameter',
+   'sea_shoreline_wave~incoming~deepwater__ashton_et_al_approach_angle_asymmetry_parameter')
+  
+  >>> waves.output_var_names
+  ('sea_surface_water_wave__min_of_increment_of_azimuth_angle_of_opposite_of_phase_velocity',
+   'sea_surface_water_wave__azimuth_angle_of_opposite_of_phase_velocity',
+   'sea_surface_water_wave__mean_of_increment_of_azimuth_angle_of_opposite_of_phase_velocity',
+   'sea_surface_water_wave__max_of_increment_of_azimuth_angle_of_opposite_of_phase_velocity',
+   'sea_surface_water_wave__height',
+   'sea_surface_water_wave__period')
+
+In each case,
+the variable names are returned in a tuple.
+The names tend to be quite descriptive,
+in order to aid in semantic matching between models.
+In practice,
+it's often convenient to use a common short name for a variable
+instead of its Standard Name.
+
+
+Getting and setting variables
+-----------------------------
+
+The values of variables exposed by a model
+can be accessed with the *get_value* method
+and modified with the *set_value* method.
+Each of these methods takes a variable name
+(a `CSDMS Standard Name`_) as input.
+
+As shown in the section above,
+the variable ``sea_surface_water_wave__height``
+is both an input and an output variable in Waves.
+Find its current value:
+
+.. code-block:: python
+
+  >>> waves.get_value('sea_surface_water_wave__height')
+  array([ 2.])
+
+In *pymt*,
+variable values are stored as `NumPy`_ arrays.
+
+Assign a new wave height value in the model:
+
+.. code-block:: python
+
+  >>> waves.set_value('sea_surface_water_wave__height', 3.5)
+
+and check the result with *get_value*:
+
+.. code-block:: python
+
+  >>> waves.get_value('sea_surface_water_wave__height')
+  array([ 3.5])
+
+
+.. Links
+
+.. _CEM: https://csdms.colorado.edu/wiki/Model:CEM
+.. _Waves: https://csdms.colorado.edu/wiki/Model_help:Waves
+.. _package: https://docs.python.org/3/glossary.html#term-package
+.. _imported: https://docs.python.org/3/glossary.html#term-importing
+.. _instance: https://en.wikipedia.org/wiki/Instance_(computer_science)
+.. _object: https://docs.python.org/3/glossary.html#term-object
+.. _properties: https://en.wikipedia.org/wiki/Property_(programming)
+.. _methods: https://en.wikipedia.org/wiki/Method_(computer_programming)
+.. _Basic Model Interface: https://csdms.colorado.edu/wiki/BMI_Description
+.. _UDUNITS: https://www.unidata.ucar.edu/software/udunits
+.. _CSDMS Standard Names: https://csdms.colorado.edu/wiki/CSDMS_Standard_Names
+.. _CSDMS Standard Name: https://csdms.colorado.edu/wiki/CSDMS_Standard_Names
+.. _NumPy: http://www.numpy.org/