Merge pull request #231 from UW-Hydro/develop

Update master in anticipation of v2.3.0

docs/configuration.rst

@@ -4,7 +4,7 @@ Configuration Specifications
 ============================
 This page documents the various options and
 parameters that can be set in the configuration
-file.
+file. An example configuration file can be found on the examples page.
 
 MetSim Section
 --------------
@@ -108,69 +108,63 @@ available at: `<https://zenodo.org/record/1402223#.XEI-mM2IZPY>`.  For more
 information about the "triangle" method see :doc:`PtriangleMethod.pdf`.
 
 For more information about input and output variables see the :ref:`data` page.
+::
+
+    # Comments begin with hashtags
+    # The first non-comment line must begin with the following:
+    Metsim:
+        time_step: int
+        start: YYYY-MM-DD
+        stop: YYYY-MM-DD
+
+        # Paths to input files
+        forcing: str
+        domain: str
+        state: str
+
+        # Output file specification
+        out_dir: str
+        out_prefix: str
+
+        # Algorithmic controls
+        utc_offset: bool
+        prec_type: str
+        lw_type: str
+        lw_cloud: str
+
 
 chunks section
 --------------
 The ``chunks`` section describes how parallel computation should be grouped
 in space. For example, to parallelize over 10 by 10 chunks of latitude and
 longitude (with netcdf dimensions named ``lat`` and ``lon``, respectively) you would use:
+::
 
-.. code-block:: ini
-    [chunks]
-    lat = 10
-    lon = 10
+    chunks:
+        lat: 10
+        lon: 10
 
 Alternatively, for an HRU based run chunked into 50 element jobs you would use:
+::
 
-.. code-block:: ini
-    [chunks]
-    hru = 50
+    chunks:
+        hru: 50
 
 As a general rule of thumb, try to evenly chunk the domain in such a way that
 the number of jobs to run is some multiple of the number of processors you wish
 to run on.
 
 forcing_vars and state_vars section
 ---------------
-The ``forcing_vars`` and ``state_vars`` sections are where you can specify which variables are in your
-input data, and the corresponding symbols which MetSim will recognize. The
-format of this section depends on the value given in the ``in_fmt`` entry in
-the ``MetSim`` section of the configuration file.  See below for conventions for
-each input type.
-
-
-netcdf and data
-```````````````
-The ``in_vars`` section for NetCDF and xarray input acts as a mapping between the variable
+The ``forcing_vars`` and ``state_vars`` sections are where you can specify which
+variables are in your input data, and the corresponding symbols which MetSim will
+recognize.  The ``in_vars`` section for acts as a mapping between the variable
 names in the input dataset to the variable names expected by MetSim.  The format
-is given as ``metsim_varname = netcdf_varname``.  The minimum required variables
+is given as ``metsim_varname: netcdf_varname``.  The minimum required variables
 given have ``metsim_varname``\s corresponding to ``t_min``, ``t_max``, and
 ``prec``; these variable names correspond to minimum daily temperature (Celcius),
 maximum daily temperature (Celcius), and precipitation (mm/day).
 
-ascii
-`````
-The ``in_vars`` section for ASCII input acts similarly to the NetCDF input
-format, except for one key point.  Variables should be given as a tautology: the
-format is given as ``metsim_varname = metsim_varname``.  The order that the
-variables are given corresponds to the column numbers that they appear in the
-input files.  The minimum required variables are ``t_min``, ``t_max``, and
-``prec``; these variable names correspond to minimum daily temperature (Celcius),
-maximum daily temperature (Celcius), and precipitation (mm/day).
-
-binary
-``````
-This section has an input style for binary files that mimics the VIC version 4
-input style.  Each line is specified as ``varname = scale cdatatype``, where
-``varname`` is the name that MetSim should use for the column, ``scale`` is a
-floating point scaling factor that should be applied after conversion from
-binary to floating point; the conversion applied by the ``scale`` is applied
-after the value in the input is converted from binary to the ``cdatatype``
-specified for each variable.  Valid ``cdatatype``\s are ``signed`` and
-``unsigned``.  ``signed`` values are interpreted as values which can be positive
-or negative, whereas ``unsigned`` values are interpreted as values that can only
-be greater than or equal to zero.
-
 domain_vars section
 -------------------
 The ``domain_vars`` section is where information about the domain file is given.
@@ -184,26 +178,109 @@ a mask of valid cells in the domain, and the elevation given in meters. If
 including ``dur`` and ``t_pk`` for disaggregating daily precipitation according
 to the "triangle" method.
 
+out_vars section
+----------------
+The ``out_vars`` section is where you can specify the output variables that you
+want to include. There are two formats for this section. The first is the old format,
+which we provide backwards compatibility for. You simply specify in the top level
+``[MetSim]`` section a list of output variables with the names used by MetSim. They
+will be written out with the same names used internally. Available options are
+dependent on whether daily or subdaily output is being generated. Options for
+daily output are:
+
+- pet
+- shortwave
+- t_max
+- t_min
+- tskc
+
+Options for subdaily output are:
+
+ - prec
+ - shortwave
+ - longwave
+ - temp
+ - vapor_pressure
+ - air_pressure
+ - tskc
+ - rel_humid
+ - spec_humid
+ - wind
+
+The syntax for output specification is as follows:
+::
+
+    out_vars:
+        metsim_varname:
+            out_name: str
+            units: str
+
+unit conversions
+================
+The ``out_vars`` section allows for specification of some simple unit conversions
+for MetSim output. The allowed options are as follows (invalid options will revert
+to the default after issuing a warning):
+
+ * prec
+   - ``mm timestep-1`` (default)
+   - ``mm s-1``
+   - ``mm h-1``
+ * pet (daily output only)
+   - ``mm timestep-1`` (default)
+   - ``mm s-1``
+   - ``mm h-1``
+ * t_max (daily output only)
+   - ``C`` (default)
+   - ``K``
+ * t_min (daily output only)
+   - ``C`` (default)
+   - ``K``
+ * temp
+   - ``C`` (default)
+   - ``K``
+ * vapor_pressure
+   - ``kPa`` (default)
+   - ``hPa``
+   - ``Pa``
+ * air_pressure
+   - ``kPa`` (default)
+   - ``hPa``
+   - ``Pa``
+ * tskc (cloud fraction)
+   - ``fraction`` (default)
+   - ``%``
+ * rel_humid
+   - ``%`` (default)
+   - ``fraction``
+
 constant_vars section
 -------------------
-The ``constant_vars`` section is optional and allows you to set some of the 
-forcing inputs to a constant value. The specification simply consists of entries 
-of the form ``metsim_varname = value``, where ``value`` is a number that can be
-converted to a double. There can only be one entry per line. If the 
+The ``constant_vars`` section is optional and allows you to set some of the
+forcing inputs to a constant value. The specification simply consists of entries
+of the form ``metsim_varname: value``, where ``value`` is a number that can be
+converted to a double. There can only be one entry per line. If the
 ``metsim_varname`` corresponds to an entry that is already in the ``forcing_vars``
-section, then the constant value will take precedence. In the current 
+section, then the constant value will take precedence. In the current
 implementation there must be at least one non-constant entry in ``forcings_vars``
 (i.e. at least one entry that is not also in ``constant_vars``).
 
 For example:
-``wind = 2.0``
+::
+
+    constant_vars:
+        wind: 2.0
+
 will result in a constant wind field in the output file. In this case ``wind``
 does not need to be specified in the ``forcing_vars`` section. If it was, it
 will still be set to a constant value of 2 m/s.
 
 Similarly:
-``t_max = 30
-t_min = 10``
+::
+
+    constant_vars:
+        t_max = 30.0
+        t_min = 10.0
+
 will result in output with a diurnal cycle in which the temperature varies at
-all locations between 10C and 30C. However, all estimation and disaggregation 
-routines are still evaluated, with constant ``t_max`` and ``t_min`` as input.
+all locations between 10C and 30C. However, all estimation and disaggregation
+routines are still evaluated, with constant ``t_max`` and ``t_min`` as input.