[release/public-v2.1.0] Documentation Updates (#483)

* update some links/version references; add list of v2.1.0 features

* add citation

* add not re: spack-stack support

* update most links for release

* edit Glossary

* document devclean, update FAQ

* change config.sh to .yaml

* reorder FAQ

* FAQ updates

* FAQ updates

* Rocoto Ch edits

* Quickstart edits

* add table label/Xlink

* update FAQ cycle-ind tasks

* fix code-block format

* update WM links

* Graphics, I/O updates, other minor

* minor updates to Graphics & Intro

* minor intro fixes

* QS updates

* misc minor edits

* edits to FV3LAM

* Update user-defined grid example & some config params

* update components ch and version #'s throughout

* update container name, minor I/O updates

* minor container updates

* several minor fixes

* update I/O input path image

* update I/O input path image

* I/O updates esp for UPP

* edits for loading graphics env

* graphics env changes; I/O python syntax update

* I/O & graphics updates

* Documentation updates for Mac and Linux

* misc updates

* add draft of CCPP updates

* misc updates

* misc updates

* rm old img

* add updated img

* fix img

* fix img

* minor updates to WE2E & CCPP note

* readme edits

* update readme & intro

* add predefined vs custom grid note

* add wrapper commands, LAM custom grid notes, remove comments throughout

* add note to manual/wrapper run section

* Update BuildSRW.rst

Correcting the text

* Update RunSRW.rst

Some text corrections

* add hpc-stack doc link; other minor updates

* update links & remove comments

* minor edits to build/run

* BuildSRW edits

* BuildSRW updates

* BuildSRW updates

* Added documentation notes for generic Linux

* Formatting corrections

* final I/O edits, RunSRW

* final Build/Run edits for mac/linux

* minor corrections

* remove Contributor's Guide

* fix */ for cron

Co-authored-by: gspetro <[email protected]>
Co-authored-by: Natalie Perlin <[email protected]>

README.md

@@ -1,15 +1,26 @@
 # UFS Short-Range Weather Application
 
-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://ufscommunity.org/.
 
-The UFS includes multiple applications (see a complete list at https://ufscommunity.org/science/aboutapps/) that support different forecast durations and spatial domains. This documentation describes the development branch of the UFS Short-Range Weather (SRW) Application, which targets predictions of atmospheric behavior on a limited spatial domain and on time scales from minutes to several days. The development branch of the application is continually evolving as the system undergoes open development. The latest SRW App release (v2.0.0) represents a snapshot of this continuously evolving system. 
+The UFS includes multiple applications (see a complete list at https://ufscommunity.org/science/aboutapps/) that support different forecast durations and spatial domains. This documentation describes the v2.1.0 release branch of the UFS Short-Range Weather (SRW) Application, which targets predictions of atmospheric behavior on a limited spatial domain and on time scales from minutes to several days. The development branch of the application is continually evolving as the system undergoes open development. The latest SRW App release (v2.1.0) represents a snapshot of this continuously evolving system. 
 
-The UFS SRW App User's Guide associated with the development branch is at: https://ufs-srweather-app.readthedocs.io/en/develop/, while the guide specific to the SRW App v2.0.0 release can be found at: https://ufs-srweather-app.readthedocs.io/en/release-public-v2/. The repository is at: https://github.com/ufs-community/ufs-srweather-app.
+This v2.1.0 release includes:
 
-For instructions on how to clone the repository, build the code, and run the workflow, see:
-https://github.com/ufs-community/ufs-srweather-app/wiki/Getting-Started
+   * Bug fixes since the v2.0.0 release
+   * Conversion to a Python workflow (from the former shell workflow)
+   * Improved container support, including the option to run across compute nodes using Rocoto
+   * Updates to CCPP that target the top of the `main` branch (which is ahead of CCPP v6.0.0). 
+   * Support for the UPP inline post option
+   * Addition of a multi-purpose code clean-up script (`devclean.sh`) 
+   * Documentation updates to reflect the changes above
 
-UFS Development Team. (2022, June 23). Unified Forecast System (UFS) Short-Range Weather (SRW) Application (Version v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.6505854
+Future work will expand the capabilities of the application to include data assimilation (DA) and a forecast restart/cycling capability. 
+
+For instructions on how to clone the repository, build the code, and run the workflow, view the instructions in the SRW App User's Guide. The UFS SRW App User's Guide specific to the SRW App v2.1.0 release can be found at: https://ufs-srweather-app.readthedocs.io/en/release-public-v2.1.0/, while the documentation for the development branch is at: https://ufs-srweather-app.readthedocs.io/en/develop/. The repository is at: https://github.com/ufs-community/ufs-srweather-app.
+
+The SRW App v2.1.0 citation is as follows and should be used when presenting results based on research conducted with the App:
+
+UFS Development Team. (2022, Nov. 17). Unified Forecast System (UFS) Short-Range Weather (SRW) Application (Version v2.1.0). Zenodo. https://doi.org/10.5281/zenodo.7277602
 
 [![Python unittests](https://github.com/ufs-community/ufs-srweather-app/actions/workflows/python_unittests.yaml/badge.svg)](https://github.com/ufs-community/ufs-srweather-app/actions/workflows/python_unittests.yaml)
 [![Python functional tests](https://github.com/ufs-community/ufs-srweather-app/actions/workflows/python_func_tests.yaml/badge.svg)](https://github.com/ufs-community/ufs-srweather-app/actions/workflows/python_func_tests.yaml)