[develop]: Adding in the tutorial for the Halloween Storm

doc/ContribGuide/contributing.rst

@@ -11,7 +11,7 @@ Fork and PR Overview
 
 Contributions to the ``ufs-srweather-app`` project are made via a :github-docs:`Fork<pull-requests/collaborating-with-pull-requests/working-with-forks/about-forks>` and :github-docs:`Pull Request (PR)<pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests>` model. GitHub provides a thorough description of this contribution model in their `Contributing to a project` :github-docs:`Quickstart<get-started/exploring-projects-on-github/contributing-to-a-project>`, but the steps, with respect to ``ufs-srweather-app`` contributions, can be summarized as:
 
-#. :github-docs:`Create an issue <issues/tracking-your-work-with-issues/creating-an-issue>` to document proposed changes.
+#. :github-docs:`Create an issue <issues/tracking-your-work-with-issues/using-issues/creating-an-issue>` to document proposed changes.
 #. :github-docs:`Fork<get-started/exploring-projects-on-github/contributing-to-a-project#forking-a-repository>` the :srw-repo:`ufs-srweather-app repository<>` into your personal GitHub account.
 #. :github-docs:`Clone<get-started/exploring-projects-on-github/contributing-to-a-project>` your fork onto your development system.
 #. :github-docs:`Create a branch<get-started/exploring-projects-on-github/contributing-to-a-project#creating-a-branch-to-work-on>` in your clone for your changes. All development should take place on a branch, *not* on ``develop``. 

doc/UsersGuide/BackgroundInfo/Components.rst

@@ -38,12 +38,12 @@ Supported model resolutions in this release include 3-, 13-, and 25-km predefine
 Model Physics
 ---------------
 
-The Common Community Physics Package (CCPP), described `here <https://dtcenter.org/community-code/common-community-physics-package-ccpp>`__, supports interoperable atmospheric physics and land surface model options. Atmospheric physics are a set of numerical methods describing small-scale processes such as clouds, turbulence, radiation, and their interactions. The most recent SRW App release (|latestr|) included five supported physics suites: FV3_RRFS_v1beta, FV3_GFS_v16, FV3_WoFS_v0, FV3_HRRR, and FV3_RAP. The FV3_RRFS_v1beta physics suite is being tested for use in the future operational implementation of the Rapid Refresh Forecast System (:term:`RRFS`) planned for 2023-2024, and the FV3_GFS_v16 is an updated version of the physics suite used in the operational Global Forecast System (GFS) v16. A detailed list of CCPP updates since the SRW App v2.1.0 release is available :ref:`here <CCPPUpdates>`. A full scientific description of CCPP parameterizations and suites can be found in the `CCPP Scientific Documentation <https://dtcenter.ucar.edu/GMTB/UFS_SRW_App_v2.2.0/sci_doc/index.html>`__, and CCPP technical aspects are described in the :doc:`CCPP Technical Documentation <ccpp-techdoc:index>`. The model namelist has many settings beyond the physics options that can optimize various aspects of the model for use with each of the supported suites. Additional information on Stochastic Physics options is available :doc:`here <stochphys:index>`. 
+The Common Community Physics Package (CCPP), described `here <https://dtcenter.org/community-code/common-community-physics-package-ccpp>`_, supports interoperable atmospheric physics and land surface model options. Atmospheric physics are a set of numerical methods describing small-scale processes such as clouds, turbulence, radiation, and their interactions. The most recent SRW App release (|latestr|) included five supported physics suites: FV3_RRFS_v1beta, FV3_GFS_v16, FV3_WoFS_v0, FV3_HRRR, and FV3_RAP. The FV3_RRFS_v1beta physics suite is being tested for use in the future operational implementation of the Rapid Refresh Forecast System (:term:`RRFS`) planned for 2023-2024, and the FV3_GFS_v16 is an updated version of the physics suite used in the operational Global Forecast System (GFS) v16. A detailed list of CCPP updates since the SRW App v2.1.0 release is available :ref:`here <CCPPUpdates>`. A full scientific description of CCPP parameterizations and suites can be found in the `CCPP Scientific Documentation <https://dtcenter.ucar.edu/GMTB/UFS_SRW_App_v2.2.0/sci_doc/index.html>`_, and CCPP technical aspects are described in the :doc:`CCPP Technical Documentation <ccpp-techdoc:index>`. The model namelist has many settings beyond the physics options that can optimize various aspects of the model for use with each of the supported suites. Additional information on Stochastic Physics options is available :doc:`here <stochphys:index>`. 
 
 .. note::
    SPP is currently only available for specific physics schemes used in the RAP/HRRR physics suite. Users need to be aware of which physics suite definition file (:term:`SDF`) is chosen when turning this option on. Among the supported physics suites, the full set of parameterizations can only be used with the ``FV3_HRRR`` option for ``CCPP_PHYS_SUITE``.
 
-Additionally, a CCPP single-column model (`CCPP-SCM <https://github.com/NCAR/ccpp-scm>`__) option has also been developed as a child repository. Users can refer to the `CCPP Single Column Model User and Technical Guide <https://github.com/NCAR/ccpp-scm/blob/main/scm/doc/TechGuide/main.pdf>`__ for more details. This CCPP-SCM user guide contains a Quick Start Guide with instructions for obtaining the code, compiling, and running test cases, which include five standard test cases and two additional FV3 replay cases (refer to section 5.2 in the CCPP-SCM user guide for more details). Moreover, the CCPP-SCM supports a precompiled version in a docker container, allowing it to be easily executed on NOAA's cloud computing platforms without any issues (see section 2.5 in the CCPP-SCM user guide for more details).
+Additionally, a CCPP single-column model (`CCPP-SCM <https://github.com/NCAR/ccpp-scm>`_) option has also been developed as a child repository. Users can refer to the `CCPP Single Column Model User and Technical Guide <https://ccpp-scm.readthedocs.io/en/latest/>`_ for more details. This CCPP-SCM user guide contains a Quick Start Guide with instructions for obtaining the code, compiling, and running test cases, which include five standard test cases and two additional FV3 replay cases (refer to section 5.2 in the CCPP-SCM user guide for more details). Moreover, the CCPP-SCM supports a precompiled version in a docker container, allowing it to be easily executed on NOAA's cloud computing platforms without any issues (see section 2.5 in the CCPP-SCM user guide for more details).
 
 The SRW App supports the use of both :term:`GRIB2` and :term:`NEMSIO` input data. The UFS Weather Model ingests initial and lateral boundary condition files produced by :term:`chgres_cube` and outputs files in netCDF format on a specific projection (e.g., Lambert Conformal) in the horizontal direction and model levels in the vertical direction.
 
@@ -57,17 +57,17 @@ The Unified Post Processor (:term:`UPP`) processes raw output from a variety of
 METplus Verification Suite
 =============================
 
-The Model Evaluation Tools (MET) package is a set of statistical verification tools developed by the `Developmental Testbed Center <https://dtcenter.org/>`__ (DTC) for use by the :term:`NWP` community to help them assess and evaluate the performance of numerical weather predictions. MET is the core component of the enhanced `METplus <https://dtcenter.org/community-code/metplus>`__ verification framework; the suite also includes the associated database and display systems called METviewer and METexpress. 
+The Model Evaluation Tools (MET) package is a set of statistical verification tools developed by the `Developmental Testbed Center <https://dtcenter.org/>`_ (DTC) for use by the :term:`NWP` community to help them assess and evaluate the performance of numerical weather predictions. MET is the core component of the enhanced `METplus <https://dtcenter.org/community-code/metplus>`_ verification framework; the suite also includes the associated database and display systems called METviewer and METexpress. 
 
-The METplus verification framework has been integrated into the SRW App to facilitate forecast evaluation. METplus is a verification framework that spans a wide range of temporal scales (warn-on-forecast to climate) and spatial scales (storm to global). It is supported by the `Developmental Testbed Center (DTC) <https://dtcenter.org/>`__. 
+The METplus verification framework has been integrated into the SRW App to facilitate forecast evaluation. METplus is a verification framework that spans a wide range of temporal scales (warn-on-forecast to climate) and spatial scales (storm to global). It is supported by the `Developmental Testbed Center (DTC) <https://dtcenter.org/>`_. 
 
 METplus comes preinstalled with :term:`spack-stack` but can also be installed on other systems individually or as part of :term:`HPC-Stack` installation. Users on systems without a previous installation of METplus can follow the :ref:`MET Installation Guide <met:installation>` and :ref:`METplus Installation Guide <metplus:install>` for individual installation. Currently, METplus *installation* is only supported as part of spack-stack installation; users attempting to install METplus individually or as part of HPC-Stack will need to direct assistance requests to the METplus team. However, METplus *use* is supported on any system with a functioning METplus installation.
 
-The core components of the METplus framework include the statistical driver (MET), the associated database and display systems known as METviewer and METexpress, and a suite of Python wrappers to provide low-level automation and examples, also called use cases. MET is a set of verification tools developed for use by the :term:`NWP` community. It matches up gridded forecast fields with either gridded analyses or point observations and applies configurable methods to compute statistics and diagnostics. Extensive documentation is available in the :doc:`METplus User's Guide <metplus:index>` and :doc:`MET User's Guide <met:index>`. Documentation for all other components of the framework can be found at the *Documentation* link for each component on the METplus `downloads <https://dtcenter.org/community-code/metplus/download>`__ page.
+The core components of the METplus framework include the statistical driver (MET), the associated database and display systems known as METviewer and METexpress, and a suite of Python wrappers to provide low-level automation and examples, also called use cases. MET is a set of verification tools developed for use by the :term:`NWP` community. It matches up gridded forecast fields with either gridded analyses or point observations and applies configurable methods to compute statistics and diagnostics. Extensive documentation is available in the :doc:`METplus User's Guide <metplus:index>` and :doc:`MET User's Guide <met:index>`. Documentation for all other components of the framework can be found at the *Documentation* link for each component on the METplus `downloads <https://dtcenter.org/community-code/metplus/download>`_ page.
 
 Among other techniques, MET provides the capability to compute standard verification scores for comparing deterministic gridded model data to point-based and gridded observations. It also provides ensemble and probabilistic verification methods for comparing gridded model data to point-based or gridded observations. Verification tasks to accomplish these comparisons are defined in the SRW App in :numref:`Table %s <VXWorkflowTasksTable>`. Currently, the SRW App supports the use of :term:`NDAS` observation files (which include conventional point-based surface and upper-air data) `in prepBUFR format <https://nomads.ncep.noaa.gov/pub/data/nccf/com/nam/prod/>`__ for point-based verification. It also supports gridded Climatology-Calibrated Precipitation Analysis (:term:`CCPA`) data for accumulated precipitation evaluation and Multi-Radar/Multi-Sensor (:term:`MRMS`) gridded analysis data for composite reflectivity and :term:`echo top` verification.
 
-METplus is being actively developed by :term:`NCAR`/Research Applications Laboratory (RAL), NOAA/Earth Systems Research Laboratories (`ESRL <https://www.esrl.noaa.gov/>`__), and NOAA/Environmental Modeling Center (:term:`EMC`), and it is open to community contributions. More details about METplus can be found on the `METplus website <https://dtcenter.org/community-code/metplus>`__.
+METplus is being actively developed by :term:`NCAR`/Research Applications Laboratory (RAL), NOAA/Earth Systems Research Laboratories (`ESRL <https://www.esrl.noaa.gov/>`__), and NOAA/Environmental Modeling Center (:term:`EMC`), and it is open to community contributions. More details about METplus can be found on the `METplus website <https://dtcenter.org/community-code/metplus>`_.
 
 Air Quality Modeling (AQM) Utilities
 =======================================

doc/UsersGuide/BackgroundInfo/Introduction.rst

@@ -4,9 +4,9 @@
 Introduction
 ==============
 
-The Unified Forecast System (:term:`UFS`) is a community-based, coupled, comprehensive Earth modeling system. NOAA's operational model suite for numerical weather prediction (:term:`NWP`) is quickly transitioning to the UFS from a number of different modeling systems. The UFS enables research, development, and contribution opportunities within the broader :term:`Weather Enterprise` (including government, industry, and academia). For more information about the UFS, visit the `UFS Portal <https://ufscommunity.org/>`__.
+The Unified Forecast System (:term:`UFS`) is a community-based, coupled, comprehensive Earth modeling system. NOAA's operational model suite for numerical weather prediction (:term:`NWP`) is quickly transitioning to the UFS from a number of different modeling systems. The UFS enables research, development, and contribution opportunities within the broader :term:`Weather Enterprise` (including government, industry, and academia). For more information about the UFS, visit the `UFS Portal <https://ufs.epic.noaa.gov/>`_.
 
-The UFS includes `multiple applications <https://ufscommunity.org/science/aboutapps/>`__ that support different forecast durations and spatial domains. This documentation describes 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 most recent SRW Application includes a prognostic atmospheric model, pre- and post-processing, and a community workflow for running the system end-to-end. These components are documented within this User's Guide and supported through the `GitHub Discussions <https://github.com/ufs-community/ufs-srweather-app/discussions/categories/q-a>`__ forum. The SRW App also includes support for a verification package (METplus) for both deterministic and ensemble simulations and support for four stochastically perturbed physics schemes. 
+The UFS includes `multiple applications <https://ufs.epic.noaa.gov/applications/>`_ that support different forecast durations and spatial domains. This documentation describes 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 most recent SRW Application includes a prognostic atmospheric model, pre- and post-processing, and a community workflow for running the system end-to-end. These components are documented within this User's Guide and supported through the `GitHub Discussions <https://github.com/ufs-community/ufs-srweather-app/discussions/categories/q-a>`_ forum. The SRW App also includes support for a verification package (METplus) for both deterministic and ensemble simulations and support for four stochastically perturbed physics schemes. 
 
 Since the last release, developers have added a variety of features:
 

doc/UsersGuide/BuildingRunningTesting/BuildSRW.rst

@@ -35,7 +35,7 @@ Install the Prerequisite Software Stack
 
 Users on any sufficiently up-to-date machine with a UNIX-based operating system should be able to install the prerequisite software stack and run the SRW Application. However, a list of prerequisites is available in :numref:`Section %s <software-prereqs>` for reference. Users should install or update their system as required before attempting to install the software stack. 
 
-Currently, installation of the prerequisite software stack is supported via spack-stack on most systems. :term:`Spack-stack` is a :term:`repository` that provides a Spack-based system to build the software stack required for `UFS <https://ufscommunity.org/>`__ applications such as the SRW App. Spack-stack is the software stack validated by the UFS Weather Model (:term:`WM`), and the SRW App has likewise shifted to spack-stack for most Level 1 systems.
+Currently, installation of the prerequisite software stack is supported via spack-stack on most systems. :term:`Spack-stack` is a :term:`repository` that provides a Spack-based system to build the software stack required for `UFS <https://ufs.epic.noaa.gov/>`_ applications such as the SRW App. Spack-stack is the software stack validated by the UFS Weather Model (:term:`WM`), and the SRW App has likewise shifted to spack-stack for most Level 1 systems.
 
 .. hint::
    Skip the spack-stack installation if working on a :srw-wiki:`Level 1 system <Supported-Platforms-and-Compilers>` (e.g., Hera, Jet, Derecho, NOAA Cloud), and :ref:`continue to the next section <DownloadSRWApp>`.

doc/UsersGuide/BuildingRunningTesting/Quickstart.rst

@@ -50,13 +50,9 @@ For a detailed explanation of how to build and run the SRW App on any supported
 
    #. Load the python environment for the workflow. Users on Level 2-4 systems will need to use one of the existing ``wflow_<platform>`` modulefiles (e.g., ``wflow_macos``) and adapt it to their system. Then, run:
 
-      .. code-block:: console
-
-         source /path/to/ufs-srweather-app/etc/lmod-setup.sh <platform>
-         module use /path/to/ufs-srweather-app/modulefiles
-         module load wflow_<platform>
-
-      where ``<platform>`` refers to a valid machine name (see :numref:`Section %s <user>`). After loading the workflow, users should follow the instructions printed to the console. For example, if the output says: 
+      .. include:: ../../doc-snippets/load-env.rst
+
+      After loading the workflow, users should follow the instructions printed to the console. For example, if the output says: 
 
       .. code-block:: console