Update documentation for GCPy 1.4.0 release

docs/source/Benchmark.rst
- Add missing section about make_benchmark_mass_table function

docs/source/Getting-Started-with-GCPy.rst
- Replace "bob" with "YOUR-USER-NAME" in MambaForge installation example
- Add section about setting the MPLBACKEND environment variable

docs/source/Guide-to-Useful-Capabilities.rst
- Fixed typo: "eegridding" -> "regridding"

docs/source/Regridding.rst
- Add note to use the offline regridding weights method if regridding to
  or from GCHP stretched grid restart files

Signed-off-by: Bob Yantosca <[email protected]>

docs/source/Benchmarking.rst

@@ -1174,13 +1174,94 @@ inventory) from the output of GEOS-Chem benchmark simulations.
 
        """
 
+.. _bmk-funcs-table-mass:
+
+make_benchmark_mass_tables
+--------------------------
+
+This function creates tables of total mass for species in two
+different GEOS-Chem benchmark simulations.
+
+.. code-block:: python
+
+   def make_benchmark_mass_tables(
+           ref,
+           refstr,
+           dev,
+           devstr,
+           varlist=None,
+           dst="./benchmark",
+           subdst=None,
+           overwrite=False,
+           verbose=False,
+           label="at end of simulation",
+           spcdb_dir=os.path.dirname(__file__),
+           ref_met_extra=None,
+           dev_met_extra=None
+   ):
+       """
+       Creates a text file containing global mass totals by species and
+       category for benchmarking purposes.
+
+       Args:
+           reflist: str
+               Pathname that will constitute
+               the "Ref" (aka "Reference") data set.
+           refstr: str
+               A string to describe ref (e.g. version number)
+           dev: list of str
+               Pathname that will constitute
+               the "Dev" (aka "Development") data set.  The "Dev"
+               data set will be compared against the "Ref" data set.
+           devstr: str
+               A string to describe dev (e.g. version number)
+
+       Keyword Args (optional):
+           varlist: list of str
+               List of variables to include in the list of totals.
+               If omitted, then all variables that are found in either
+               "Ref" or "Dev" will be included.  The varlist argument
+               can be a useful way of reducing the number of
+               variables during debugging and testing.
+               Default value: None
+           dst: str
+               A string denoting the destination folder where the file
+               containing emissions totals will be written.
+               Default value: ./benchmark
+           subdst: str
+               A string denoting the sub-directory of dst where PDF
+               files containing plots will be written.  In practice,
+               subdst is only needed for the 1-year benchmark output,
+               and denotes a date string (such as "Jan2016") that
+               corresponds to the month that is being plotted.
+               Default value: None
+           overwrite: bool
+               Set this flag to True to overwrite files in the
+               destination folder (specified by the dst argument).
+               Default value: False
+           verbose: bool
+               Set this flag to True to print extra informational output.
+               Default value: False.
+           spcdb_dir: str
+               Directory of species_datbase.yml file
+               Default value: Directory of GCPy code repository
+           ref_met_extra: str
+               Path to ref Met file containing area data for use with restart files
+               which do not contain the Area variable.
+               Default value: ''
+           dev_met_extra: str
+               Path to dev Met file containing area data for use with restart files
+               which do not contain the Area variable.
+               Default value: ''
+       """
+
 .. _bmk-funcs-table-accum:
 
 make_benchmark_mass_accumulation_tables
 ---------------------------------------
 
-This function creates tables of total mass for species in two
-different data set from GEOS-Chem benchmark simulation output.
+This function creates tables of mass accumulation over time for species in two
+different GEOS-Chem benchmark simulations.
 
 .. code-block:: python
 
@@ -1260,6 +1341,7 @@ different data set from GEOS-Chem benchmark simulation output.
            YAML file called "species_database.yml".
        """
 
+
 .. _bmk-funcs-table-cons:
 
 make_benchmark_mass_conservation_table

docs/source/Getting-Started-with-GCPy.rst

@@ -226,7 +226,7 @@ Linux and Windows Subsystem for Linux
      - Press ENTER to confirm the location
      - Press CTRL-C to abort the installation
      - Or specify a different location below
-     [/home/bob/mambaforge] >>>
+     [/home/YOUR-USER-NAME/mambaforge] >>>
 
    In most cases, it should be OK to accept the default installation
    location.  But on some systems, users may be encouraged to install
@@ -366,7 +366,7 @@ Follow these steps:
    locations of Python libraries on your system that were not
    installed by :program:`Mamba`.
 
-   Add the path to your GCPy source code folder  :file:`~/.bashrc` file:
+   Add the path to your GCPy source code folder :file:`~/.bashrc` file:
 
    .. code-block:: bash
 
@@ -381,6 +381,28 @@ Follow these steps:
    to apply the change. |br|
    |br|
 
+#. **Set the** :envvar:`MPLBACKEND` **environment variable**
+
+   The environment variable :envvar:`MPLBACKEND` specifies the X11
+   backend that the Matplotlib package will use to render plots to the
+   screen.
+
+   Add this line to your :file:`~/.bashrc` file on your local PC/Mac
+   and on any remote computer systems where you will use GCPy:
+
+   .. code-block:: bash
+
+      export MPLBACKEND=tkagg
+
+   And then use:
+
+   .. code-block:: console
+
+      $ source ~/.bashrc
+
+   to apply the change. |br|
+   |br|
+
 #. **Perform a simple test:**
 
    Run the following commands in your terminal to check if the

docs/source/Guide-to-Useful-Capabilities.rst

@@ -215,7 +215,7 @@ Regridding
 
 .. _capabilities-regridding-rules:
 
-General eegridding rules
+General regridding rules
 ------------------------
 
 GCPy supports regridding between all horizontal GEOS-Chem grid types,

docs/source/Regridding.rst

@@ -51,6 +51,12 @@ directly from the command line (:ref:`see the examples below
 <regrid-classic-example>`) or from a Python script or
 interpreter (:code:`gcpy.file_regrid.file_regrid()`)
 
+.. note::
+
+   For regridding to or from GCHP stretched-grid restart files, we
+   recommend using the :ref:`offline regridding weights method
+   <regrid-gchp>`.
+
 The syntax of :code:`file_regrid` is as follows:
 
 .. code-block:: python