Merge pull request #1 from MichaelLueken/doc/FAQ_update

Update conf.py to address new broken link

Author: selbigmtnwx23

Externals.cfg

@@ -12,7 +12,7 @@ protocol = git
 repo_url = https://github.com/ufs-community/ufs-weather-model
 # Specify either a branch name or a hash but not both.
 #branch = develop
-hash = 855243a
+hash = 826f6ff
 local_path = sorc/ufs-weather-model
 required = True
 

doc/UsersGuide/BackgroundInfo/Components.rst

@@ -132,7 +132,7 @@ Build System and Workflow
 
 The SRW Application has a portable, CMake-based build system that packages together all the components required to build the SRW Application. This build system collects the components necessary for running the end-to-end SRW Application, including the UFS Weather Model and the pre- and post-processing software. Additional libraries necessary for the application (e.g., :term:`NCEPLIBS-external` and :term:`NCEPLIBS`) are not included in the SRW Application build system but are available pre-built on pre-configured platforms. On other systems, they can be installed via spack-stack (see :doc:`spack-stack Documentation <spack-stack:index>`). There is a small set of :ref:`prerequisite system libraries <software-prereqs>` and utilities that are assumed to be present on the target computer: the CMake build software; a Fortran, C, and C++ compiler; and an :term:`MPI` library.
 
-Once built, users can generate a Rocoto-based workflow that will run each task in the proper sequence (see :numref:`Chapter %s <RocotoInfo>` or the `Rocoto documentation <https://github.com/christopherwharrop/rocoto/wiki/Documentation>`__ for more information on Rocoto and workflow management). If Rocoto and/or a batch system is not present on the available platform, the individual components can be run in a stand-alone, command line fashion with provided run scripts. 
+Once built, users can generate a Rocoto-based workflow that will run each task in the proper sequence (see :numref:`Chapter %s <RocotoInfo>` or the `Rocoto documentation <https://github.com/NOAA-GSL/rocoto/wiki/Documentation>`__ for more information on Rocoto and workflow management). If Rocoto and/or a batch system is not present on the available platform, the individual components can be run in a stand-alone, command line fashion with provided run scripts. 
 
 The SRW Application allows users to configure various elements of the workflow. For example, users can modify the parameters of the atmospheric model, such as start and end dates, duration, integration time step, and the physics suite used for the simulation. It also allows for configuration of other elements of the workflow; for example, users can choose whether to run some or all of the pre-processing, forecast model, and post-processing steps. More information on how to configure the workflow is available in :numref:`Section %s <UserSpecificConfig>`.
 

doc/UsersGuide/CustomizingTheWorkflow/DefineWorkflow.rst

@@ -6,7 +6,7 @@ Defining an SRW App Workflow
 
 Many predefined workflows with optional variants exist within the Short-Range Weather Application, but the Application also includes the ability to define a new workflow from scratch. This functionality allows users to add tasks to the workflow to meet their scientific exploration needs.
 
-Rocoto is the primary workflow manager software used by the UFS SRW App. Rocoto workflows are defined in an XML file (``FV3LAM_wflow.xml``) based on parameters set during experiment generation. The SRW Rocoto XML is built using the UW Tools Rocoto Tool. Reference its documentation `here <https://uwtools.readthedocs.io/en/main/sections/user_guide/yaml/rocoto.html>`__. For more information about Rocoto, check out its `documentation here <http://christopherwharrop.github.io/rocoto/>`_.
+Rocoto is the primary workflow manager software used by the UFS SRW App. Rocoto workflows are defined in an XML file (``FV3LAM_wflow.xml``) based on parameters set during experiment generation. The SRW Rocoto XML is built using the UW Tools Rocoto Tool. Reference its documentation `here <https://uwtools.readthedocs.io/en/main/sections/user_guide/yaml/rocoto.html>`__. For more information about Rocoto, check out its `documentation here <https://noaa-gsl.github.io/rocoto/>`_.
 
 Order of Precedence
 ===================

doc/UsersGuide/Reference/Glossary.rst

@@ -264,7 +264,7 @@ Glossary
       A central location in which files (e.g., data, code, documentation) are stored and managed.
 
    Rocoto
-      The `Rocoto Workflow Management System <https://github.com/christopherwharrop/rocoto/wiki/documentation>`__ is a Ruby-based tool that manages workflow task dependencies and job submission on :term:`HPC` systems. Rocoto communicates with batch systems to run tasks in the proper sequence based on dependencies and can automatically resubmit failed tasks. The SRW App uses Rocoto to orchestrate the execution of workflow tasks defined in the ``FV3LAM_wflow.xml`` file. For more information, see :numref:`Section %s <RocotoInfo>`.
+      The `Rocoto Workflow Management System <https://github.com/NOAA-GSL/rocoto/wiki/Documentation>`__ is a Ruby-based tool that manages workflow task dependencies and job submission on :term:`HPC` systems. Rocoto communicates with batch systems to run tasks in the proper sequence based on dependencies and can automatically resubmit failed tasks. The SRW App uses Rocoto to orchestrate the execution of workflow tasks defined in the ``FV3LAM_wflow.xml`` file. For more information, see :numref:`Section %s <RocotoInfo>`.
 
    RRFS
       The `Rapid Refresh Forecast System <https://gsl.noaa.gov/research/predictions>`_ (RRFS) is NOAA's next-generation convection-allowing, rapidly-updated, ensemble-based data assimilation and forecasting system currently scheduled for operational implementation in 2024. It is designed to run forecasts on a 3-km :term:`CONUS` domain, see also `NOAA Rapid Refresh Forecast System (RRFS) <https://registry.opendata.aws/noaa-rrfs/>`__. Experimental data is currently available from the `AWS S3 NOAA-RRFS  <https://noaa-rrfs-pds.s3.amazonaws.com/index.html#rrfs_a/>`__ bucket for deterministic forecasts out to 60 hours at 00, 06, 12, and 18 UTC. Additionally, hourly forecasts out to 18 hours may be available for more recent RRFS model runs; the user needs to verify that data exists for needed dates.

doc/UsersGuide/Reference/RocotoInfo.rst

@@ -9,7 +9,7 @@ Rocoto is a Ruby program that communicates with the batch system on an
 :term:`HPC` system to run and manage dependencies between the tasks. Rocoto submits jobs to the HPC batch
 system as the task dependencies allow and runs one instance of the workflow for a set of user-defined
 :term:`cycles <cycle>`. More information about Rocoto can be found on the 
-`Rocoto Wiki <https://github.com/christopherwharrop/rocoto/wiki/documentation>`__.
+`Rocoto Wiki <https://github.com/NOAA-GSL/rocoto/wiki/documentation>`__.
 
 The SRW App workflow is defined in a Jinja-enabled Rocoto XML template called ``FV3LAM_wflow.xml``,
 which resides in the ``parm`` directory. When the ``generate_FV3LAM_wflow.py`` script is run, 
@@ -19,7 +19,7 @@ and task interdependencies. The generated XML file is then copied to the experim
 ``$EXPTDIR/FV3LAM_wflow.xml``.
 
 There are a number of Rocoto commands available to run and monitor the workflow; users can find more information in the
-complete `Rocoto documentation <http://christopherwharrop.github.io/rocoto/>`__.
+complete `Rocoto documentation <https://noaa-gsl.github.io/rocoto/>`__.
 Descriptions and examples of commonly used commands are discussed below.
 
 .. _RocotoRunCmd:
@@ -50,7 +50,7 @@ Users will need to include the absolute or relative path to these files when run
 It is important to note that the ``rocotorun`` process is iterative; the command must be executed
 many times before the entire workflow is completed, usually every 1-10 minutes. This command can be
 placed in the user’s :term:`crontab`, and cron will call it with a specified frequency. More information on
-this command can be found in the `Rocoto documentation <http://christopherwharrop.github.io/rocoto/>`__.
+this command can be found in the `Rocoto documentation <https://noaa-gsl.github.io/rocoto/>`__.
 
 The first time the ``rocotorun`` command is executed for a workflow, the files ``FV3LAM_wflow.db`` and
 ``FV3LAM_wflow_lock.db`` are created.  There is usually no need for the user to modify these files.
@@ -130,7 +130,7 @@ on the grid size and computational resources available), the output of the ``roc
 When the workflow runs to completion, all tasks will be marked as SUCCEEDED. The log file for each task
 is located in ``$EXPTDIR/log``. If any task fails, the corresponding log file can be checked for error
 messages. Optional arguments for the ``rocotostat`` command can be found in the 
-`Rocoto documentation <http://christopherwharrop.github.io/rocoto/>`__.
+`Rocoto documentation <https://noaa-gsl.github.io/rocoto/>`__.
 
 .. _rocotocheck:
 

doc/conf.py

@@ -127,6 +127,7 @@
                     r'https://doi.org/10.5281/zenodo.14834682',
                     r'https://www.naturalearthdata.com/downloads/',
                     r'https://www.xquartz.org/',
+                    r'https://doi.org/10.5194/gmd-14-5487-2021',
                    ]
 
 # Ignore anchor tags for SRW App data bucket. Shows Not Found even when they exist.

parm/field_table.FV3_RRFS_v1beta

@@ -3,7 +3,7 @@
  "TRACER", "atmos_mod", "sphum"
            "longname",     "specific humidity"
            "units",        "kg/kg"
-       "profile_type", "fixed", "surface_value=1.e30" /
+       "profile_type", "fixed", "surface_value=3.e-6" /
 # prognostic cloud water mixing ratio
  "TRACER", "atmos_mod", "liq_wat"
            "longname",     "cloud water mixing ratio"
@@ -33,7 +33,7 @@
  "TRACER", "atmos_mod", "water_nc"
            "longname",     "cloud liquid water number concentration"
            "units",        "/kg"
-       "profile_type", "fixed", "surface_value=1.e30" /
+       "profile_type", "fixed", "surface_value=0.0" /
 # prognostic cloud ice number concentration
  "TRACER", "atmos_mod", "ice_nc"
            "longname",     "cloud ice water number concentration"