[develop]: PI13 Documentation Update (#127)

* update intro w/code additions since v1.2.0

* update tech overview dir structure

* add info on manual vs auto submission

* several misc changes

* add plotting info

* update plotting info

* add plot images, add extlinks, misc other

* add Rocoto chapter, misc edits

* rm workflow section in DA chapter

* add misc

* minor conf.py updates

* add ConfigWorkflow chapter

* explain task parameters & configuration

* update testing ch

* update glossary

* add configworkflow chapter

* update file paths & misc in Model ch

* misc minor update in Model ch

* Update DA ch

* Update letkf_land.yaml info

* fix broken intersphinx link

* update jedi doc version

* DA ch updates

* misc minor edits

* update wflow dir structure diagram

* update wflow dir structure diagram

* add new chapters to introduction

* misc minor Intro edits

* misc tech overview edits

* misc tech overview updates

* rm uw from hierarchical repo structure?

* update table 1.1

* update L1 Build/Run ch

* L1 Build/Run ch minor/misc updates

* update container chapter

* misc minor edits

* ConfigWorkflow updates

* minor updates to reference chs

* minor misc fixes

* minor misc updates

* update docs w/changes from PR #129

* update docs w/changes from PR #129

* update docs w/changes from PR #129

* rm mention of 2019 case

* remove ERA5 model input file section

* rm vector2tile info

* add info on grid description files to DA chapter/IODA section

* rm run without rocoto section

* update wording re: landdaroot

README.md

@@ -1,6 +1,6 @@
 # UFS Offline Land Data Assimilation System
 
-The Unified Forecast System (UFS) is a community-based, coupled, comprehensive Earth modeling system. It is designed to be the source system for NOAA's operational numerical weather prediction applications while enabling research, development, and contribution opportunities for the broader Weather Enterprise. For more information about the UFS, visit the UFS Portal at https://ufscommunity.org/.
+The Unified Forecast System (UFS) is a community-based, coupled, comprehensive Earth modeling system. It is designed to be the source system for NOAA's operational numerical weather prediction applications while enabling research, development, and contribution opportunities for the broader Weather Enterprise. For more information about the UFS, visit the UFS Portal at https://ufs.epic.noaa.gov/.
 
 The UFS includes [multiple applications](https://ufscommunity.org/science/aboutapps/) that support different forecast durations and spatial domains. This repository hosts the source code for the UFS Land Data Assimilation (DA) System. Land DA is an offline version of the Noah Multi-Physics (Noah-MP) land surface model (LSM) used in the UFS Weather Model (WM). Its data assimilation framework uses the Joint Effort for Data assimilation Integration (JEDI) software stack, which includes the Object-Oriented Prediction System (OOPS) for the data assimilation algorithm, the Interface for Observation Data Access (IODA) for observation formatting and processing, and the Unified Forward Operator (UFO) for comparing model forecasts and observations. 
 

doc/source/BackgroundInfo/Introduction.rst

@@ -5,25 +5,21 @@ Introduction
 ****************
 
 This User's Guide provides guidance for running the Unified Forecast System 
-(:term:`UFS`) offline Land Data Assimilation (DA) System. Land DA is an offline version of the Noah Multi-Physics (Noah-MP) land surface model (LSM) used in the `UFS Weather Model <https://github.com/ufs-community/ufs-weather-model>`__ (WM). Its data assimilation framework uses 
-the Joint Effort for Data assimilation Integration (:term:`JEDI`) software. The offline UFS Land DA System currently only works with snow data. 
+(:term:`UFS`) offline Land Data Assimilation (DA) System. Land DA is an offline version of the Noah Multi-Physics (Noah-MP) land surface model (LSM) used in the `UFS Weather Model <https://github.com/ufs-community/ufs-weather-model>`_ (WM). Its data assimilation framework uses 
+the Joint Effort for Data assimilation Integration (:term:`JEDI`) software. Currently, the offline UFS Land DA System only works with snow data. 
 Thus, this User's Guide focuses primarily on the snow DA process.
 
-Since the last release, developers have added a variety of features:
+Since the |latestr| release, the following capabilities have been added to the Land DA System:
 
-* Integration of the UFS Noah-MP land component into the Land DA System for use as an alternative to the Common Community Physics Package (:term:`CCPP`) Noah-MP LSM land driver
-* Model forcing options for use with the UFS land component:
-
-   * Provided a new analysis option in the cubed-sphere native grid using :term:`GSWP3` forcing
-   * Established global land grid-point consistency with the head of the UFS WM baseline test cases (New global land grid point is changed from 18360 to 18322.)
-   * Added a new sample configuration file (``settings_DA_cycle_gswp3``)
-   * Included a new ECMWF :term:`ERA5` reanalysis forcing option in the existing vector-to-tile conversion analysis process
-
-* CTest suite upgrades --- the ERA5 CTests now test the operability of seven major components of Land DA: vector2tile, create_ens, letkfoi_snowda, apply_jediincr, tile2vector, land_driver, and UFS datm_land.
-* Upgrade of JEDI :term:`DA <data assimilation>` framework to use JEDI Skylab v4.0 (`PR #28 <https://github.com/ufs-community/land-DA_workflow/pull/28>`__)
-* Updates to sample datasets for the release (see the `Land DA data bucket <https://registry.opendata.aws/noaa-ufs-land-da/>`__)
-* Singularity/Apptainer container (``ubuntu20.04-intel-landda-release-public-v1.2.0``) updates to support the changes described above
-* Documentation updates to reflect the changes above
+* Added cycled run capability (:land-wflow-repo:`PR #101 <pull/101/>`)
+* Provide automated run option using cron (:land-wflow-repo:`PR #110 <pull/110>`)
+* Added analysis plotting task (:land-wflow-repo:`PR #107 <pull/107>`)
+* Upgraded to JEDI Skylab v7.0 (:land-wflow-repo:`PR #92 <pull/92/>`)
+* Upgraded to spack-stack v1.6.0 (:land-wflow-repo:`PR #102 <pull/102>`)
+* Extended container support (:land-wflow-repo:`PR #85 <pull/85>`)
+* Updated directory structure for NCO compliance (:land-wflow-repo:`PR #75 <pull/75>`)
+* Removed land driver from CTest (:land-wflow-repo:`PR #123 <pull/123>`)
+* Removed land-driver and vector2tile (:land-wflow-repo:`PR #129 <pull/129>`)
 
 The Land DA System citation is as follows and should be used when presenting results based on research conducted with the Land DA System:
 
@@ -37,8 +33,8 @@ This User's Guide is organized into four sections: (1) *Background Information*;
 
 Background Information
 ========================
-   * This chapter (Introduction) provides background information on the Unified Forecast System (:term:`UFS`) and the NoahMP model. 
-   * :numref:`Chapter %s <TechOverview>` (Technical Overview) outlines prerequisites, user support levels, and directory structure. 
+   * This chapter (Introduction) provides user support information and background information on the Unified Forecast System (:term:`UFS`) and the Noah-MP model. 
+   * :numref:`Chapter %s <TechOverview>` (Technical Overview) outlines prerequisites, supported systems, and directory structure. 
 
 Building, Running, and Testing the Land DA System
 ===================================================
@@ -50,12 +46,15 @@ Building, Running, and Testing the Land DA System
 Customizing the Workflow
 =========================
 
-   * :numref:`Chapter %s: Model <Model>` provides information on input data and configuration parameters in the Noah-MP LSM and its Vector-to-Tile Converter.
+   * :numref:`Chapter %s: Available Workflow Configuration Parameters <ConfigWorkflow>` explains all of the user-configurable options currently available in the workflow configuration file (``land_analysis*.yaml``).
+   * :numref:`Chapter %s: Model <Model>` provides information on input data and configuration parameters in the Noah-MP LSM.
    * :numref:`Chapter %s: DA Framework <DASystem>` provides information on the DA system, required data, and configuration parameters. 
 
 Reference
 ===========
 
+   * :numref:`Chapter %s: Rocoto <RocotoInfo>` provides background information on the Rocoto workflow manager as used in Land DA.  
+   * :numref:`Chapter %s: FAQ <FAQ>` addresses frequently asked questions. 
    * :numref:`Chapter %s: Glossary <Glossary>` lists important terms. 
 
 User Support and Documentation
@@ -85,10 +84,11 @@ If users (especially new users) believe they have identified a bug in the system
 Feature Requests and Enhancements
 ==================================
 
-Users who want to request a feature enhancement or the addition of a new feature have two options: 
+Users who want to request a feature enhancement or the addition of a new feature have a few options: 
 
    #. File a `GitHub Issue <https://github.com/ufs-community/land-DA_workflow/issues/new>`__ and add (or request that a code manager add) the ``EPIC Support Requested`` label. 
    #. Post a request for a feature or enhancement in the `Enhancements <https://github.com/ufs-community/land-DA_workflow/discussions/categories/enhancements>`__ category of GitHub Discussions. These feature requests will be forwarded to the Earth Prediction Innovation Center (`EPIC <https://epic.noaa.gov/>`__) management team for prioritization and eventual addition to the Land DA System. 
+   #. Email the request to support.epic@noaa.gov. 
 
 
 .. _Background:
@@ -131,7 +131,7 @@ The Noah-MP LSM has evolved through community efforts to pursue and refine a mod
 
 Noah-MP has been implemented in the UFS via the :term:`CCPP` physics package and 
 is currently being tested for operational use in GFSv17 and RRFS v2. Additionally, the UFS Weather Model now contains a Noah-MP land component. Noah-MP has 
-also been used operationally in the NOAA National Water Model (NWM) since 2016. Details about the model's physical parameterizations can be found in :cite:t:`NiuEtAl2011` (2011). 
+also been used operationally in the NOAA National Water Model (NWM) since 2016. Details about the model's physical parameterizations can be found in :cite:t:`NiuEtAl2011` (2011), and a full description of the model is available in the `Community Noah-MP Land Surface Modeling System Technical Description Version 5.0 <https://opensky.ucar.edu/islandora/object/technotes:599>`_. 
 
 Disclaimer 
 *************