Merge pull request #70 from gsketefian/community_develop

Change workflow base directory name in docs from fv3sar_workflow to r…

docs/user_guide_sphinx/source/Chapter2.rst

@@ -96,8 +96,8 @@ directory called ``${BASEDIR}``, clone the repository and check out the
 
    % mkdir ${BASEDIR}
    % cd ${BASEDIR}
-   % git clone ssh://${USER}@vlab.ncep.noaa.gov:29418/fv3sar_workflow
-   % cd fv3sar_workflow
+   % git clone ssh://${USER}@vlab.ncep.noaa.gov:29418/regional_workflow
+   % cd regional_workflow
    % git checkout community
 
 The model source code is located in the NEMSfv3gfs repository, which includes
@@ -164,14 +164,14 @@ successful run.  The hash numbers of these commits are shown in :numref:`Table %
    +-----------------+------------------+
 
 For convenience, a script named ``checkout_NEMSfv3gfs.sh`` has been created in
-the directory ``$BASEDIR/fv3sar_workflow/ush`` to perform these clone and checkout
+the directory ``$BASEDIR/regional_workflow/ush`` to perform these clone and checkout
 steps. This script can check out either the heads of the above branches or the
 specific commits listed above (the commit hashes are hard-coded into the script).
 To have it check out the commits, call this script as follows:
 
 .. code-block:: console
 
-   % cd ${BASEDIR}/fv3sar_workflow/ush
+   % cd ${BASEDIR}/regional_workflow/ush
    % ./checkout_NEMSfv3gfs.sh "hash"
 
 To have the script check out the branch heads, change the first argument from
@@ -190,15 +190,15 @@ To build the FV3SAR pre-processing utilities on theia:
 
 .. code-block:: console
 
-   % cd ${BASEDIR}/fv3sar_workflow/regional
+   % cd ${BASEDIR}/regional_workflow/regional
    % ./build_regional theia >& out.build_regional
 
 Other supported build platforms are ``"cheyenne``, ``wcoss_cray``, or ``odin``.
-When the build completes, there should be 9 executables under ``${BASEDIR}/fv3sar_workflow/exec``:
+When the build completes, there should be 9 executables under ``${BASEDIR}/regional_workflow/exec``:
 
 .. code-block:: console
 
-   % ls ${BASEDIR}/fv3sar_workflow/exec
+   % ls ${BASEDIR}/regional_workflow/exec
    filter_topo        global_chgres         make_solo_mosaic
    fregrid            make_hgrid            ml01rg2.x       
    fregrid_parallel   make_hgrid_parallel   shave.x         

docs/user_guide_sphinx/source/Chapter3.rst

@@ -1,4 +1,4 @@
-.. _config_fv3sar_workflow:
+.. _config_regional_workflow:
 
 ***************************************
 Configuring the FV3SAR Workflow
@@ -8,19 +8,19 @@ The following steps describe how to create a user-specific configuration
 file in order to un your experiment in a given environment.
 
 1. Create a user-specific configuration file named ``config.sh`` in the subdirectory
-   ``ush`` under the ``$BASEDIR/fv3sar_workflow`` directory containing appropriate
+   ``ush`` under the ``$BASEDIR/regional_workflow`` directory containing appropriate
    variable settings for your environment, experiment, etc.
 
    A configuration file named ``config_defaults.sh`` containing default values already
-   exists in the ``ush`` subdirectory (this file is part of the ``fv3sar_workflow`` 
+   exists in the ``ush`` subdirectory (this file is part of the ``regional_workflow`` 
    repository).  The setup script (called ``setup.sh`` and located in ``ush``) that
    will be called in the workflow generation step below first sources ``config_defaults.sh``
    and then sources ``config.sh`` if the latter exists.  Thus, any settings in ``config.sh``
    will overwrite the ones in ``config_defaults.sh``.
 
    Instead of creating a ``config.sh`` script with custom settings, a user can directly
    modify the variable settings in ``config_defaults.sh``.  However, we do not recommend
-   this approach because if this file is then pushed to the remote ``fv3sar_workflow``
+   this approach because if this file is then pushed to the remote ``regional_workflow``
    repository, that repository will contain in its copy of ``config_defaults.sh`` variable
    settings that are specific to your environment and/or experiment.  If others then pull
    from this repository, they will inherit these settings, but these settings will likely
@@ -44,7 +44,7 @@ file in order to un your experiment in a given environment.
    QUEUE_HPSS="service"
    QUEUE_RUN_FV3SAR="batch"
    #
-   BASEDIR="/path/to/directory/of/fv3sar_workflow/and/NEMSfv3gfs/clones"
+   BASEDIR="/path/to/directory/of/regional_workflow/and/NEMSfv3gfs/clones"
    TMPDIR="/path/to/temporary/work/directories"
    UPPDIR="/scratch3/BMC/det/beck/FV3-CAM/EMC_post/sorc/ncep_post.fd"
    CCPP="false"

docs/user_guide_sphinx/source/Chapter4.rst

@@ -1,11 +1,11 @@
-.. _running_fv3sar_workflow:
+.. _running_regional_workflow:
 
 ****************************
 Running the FV3SAR Workflow
 ****************************
 The steps described in this section assume the config.sh file
 has been created following the steps outlined in 
-section :ref:`config_fv3sar_workflow`.  In this section, the run and
+section :ref:`config_regional_workflow`.  In this section, the run and
 work directories will be created and a script to run the rocoto
 workflow will be generated to run the FV3SAR.
 
@@ -15,7 +15,7 @@ workflow will be generated to run the FV3SAR.
 
 .. code-block:: console
 
-   % cd $BASEDIR/fv3sar_workflow/ush
+   % cd $BASEDIR/regional_workflow/ush
    % generate_FV3SAR_wflow.sh
 
 This will create a run directory and a work directory, and it will
@@ -137,7 +137,7 @@ files in two specified run directories and their ``INPUT`` subdirectories.  Run
 
 .. code-block:: console
 
-   % cd $BASEDIR/fv3sar_workflow/ush
+   % cd $BASEDIR/regional_workflow/ush
    % ./cmp_rundirs_ncfiles.sh "$rundir1" "$rundir2"
 
 Here, ``rundir1`` and ``rundir2`` are the two run directories you want to compare.