Merge pull request #585 from johnsonbk/update_docs_to_bring_in_compli…

…ance_with_NSF_policy

Update documentation in accordance with NSF policy

CHANGELOG.rst

@@ -22,6 +22,15 @@ individual files.
 
 The changes are now listed with the most recent at the top.
 
+**December 1 2023 :: Bringing DART documentation in accordance with NSF Policy. Tag v10.9.2**
+
+- doc-fixes:
+
+  - Brings DART documentation in accordance with the November 2023,
+    "Official Policy on Brand Standards of the U.S. National Science
+    Foundation." Changes instances of "NCAR" to "NSF NCAR" and adds
+    NSF logo to the DART logo in the navigation menu.
+
 **November 9 2023 :: Github Actions MPIf08 Check. Tag v10.9.1**
 
 - Adds a new check to the Github Actions workflow that uses the

assimilation_code/modules/assimilation/adaptive_inflate_mod.rst

@@ -9,7 +9,7 @@ It can provide constant valued inflation in state or observation space, consiste
 provide spatially-constant, time-varying adaptive inflation. It can provide spatially-varying, time-varying adaptive
 inflation and it can provide temporally-varying observation space inflation. And finally, it can provide adaptive damped
 inflation, which decreases inflation through time when observation density varies. Diagnostic output and restart files
-are available. Several papers on the NCAR `DART <https://dart.ucar.edu/publications/>`__ website document the
+are available. Several papers on the NSF NCAR `DART <https://dart.ucar.edu/publications/>`__ website document the
 algorithms in detail. The ``DART/tutorial/section12`` chapter has more information.
 
 Details on controlling the inflation options are contained in the documentation for the filter. The filter_nml controls

conf.py

@@ -17,11 +17,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'DART'
-copyright = '2022, University Corporation for Atmospheric Research'
+copyright = '2023, University Corporation for Atmospheric Research'
 author = 'Data Assimilation Research Section'
 
 # The full version, including alpha/beta/rc tags
-release = '10.9.1'
+release = '10.9.2'
 root_doc = 'index'
 
 # -- General configuration ---------------------------------------------------
@@ -71,7 +71,7 @@
 #
 html_theme = 'sphinx_rtd_theme'
 html_show_sphinx = False
-html_logo = 'guide/_static/ncar-dart-logo-navy.svg'
+html_logo = 'guide/_static/nsf-ncar-dart.png'
 html_theme_options = {
     'logo_only': True,
     'includehidden': False

guide/available-observation-converters.rst

@@ -59,8 +59,8 @@ In addition the following external program produces DART observation sequence
 files:
 
 -  `Observation Processing And Wind Synthesis
-   (OPAWS) <http://code.google.com/p/opaws/>`__: OPAWS can process NCAR Dorade
-   (sweep) and NCAR EOL Foray (netCDF) radar data. It analyzes (grids) data in
+   (OPAWS) <http://code.google.com/p/opaws/>`__: OPAWS can process NSF NCAR Dorade
+   (sweep) and NSF NCAR EOL Foray (netCDF) radar data. It analyzes (grids) data in
    either two-dimensions (on the conical surface of each sweep) or
    three-dimensions (Cartesian). Analyses are output in netCDF, Vis5d, and/or
    DART (Data Assimilation Research Testbed) formats.

guide/benefits-of-using-dart.rst

@@ -66,7 +66,7 @@ Here are some of the many benefits of using DART:
    functionality, so for this purpose it is best to first get in touch with the
    DART team at dart @ ucar.edu to make the process as smooth as possible.
 7. Finally, and perhaps most importantly, DART **has world-class support**
-   available from the DART team at NCAR. A talented team of dedicated software
+   available from the DART team at NSF NCAR. A talented team of dedicated software
    engineers and data assimilation scientists work together to continually
    improve DART and support user needs. See the `About page <https://dart.ucar.edu/about/>`__ for
    more information about the DART team.

guide/brief-history-of-dart.rst

@@ -2,7 +2,7 @@ A brief history of DART
 =======================
 
 The DART project was initiated in August 2001, and in 2003, the Data
-Assimilation Research Section (DAReS) was officially formed at NCAR. In 2004,
+Assimilation Research Section (DAReS) was officially formed at NSF NCAR. In 2004,
 the first officially supported version of DART was released. Consistent version
 control history is available back to 2005, making DART an extremely long-lived
 and well-supported software project. Since 2004, there have been more than a

guide/creating-obs-seq-real.rst

@@ -114,7 +114,7 @@ Data sources and formats
 See the various subdirectories here, which generally include information on
 where the example data was obtained and in what format it is distributed. Most
 data is available for download off the web. The Data Support Section (DSS) at
-NCAR has large data repositories, the MADIS data center distributes observations
+NSF NCAR has large data repositories, the MADIS data center distributes observations
 in netCDF format, GTS real-time weather data is available from various sources.
 For new converters, if you can find what format the data is distributed in you
 may be able to adapt one of the existing converters here for your own use.

index.rst

@@ -6,8 +6,8 @@ Welcome to the Data Assimilation Research Testbed
 The Data Assimilation Research Testbed (DART) is an open-source, freely
 available community facility for ensemble data assimilation (DA). [1]_ DART is
 developed and maintained by the `Data Assimilation Research Section
-(DAReS) <https://dart.ucar.edu/about/>`_ at the `National Center
-for Atmospheric Research (NCAR) <https://ncar.ucar.edu>`_.
+(DAReS) <https://dart.ucar.edu/about/>`_ at the NSF `National Center
+for Atmospheric Research (NSF NCAR) <https://ncar.ucar.edu>`_.
 
 +------------------------------+------------------------------+
 | |spaghetti_square|           | |assim_anim|                 |

models/POP/readme.rst

@@ -13,7 +13,7 @@ of POP:
   (CESM POP2; Smith et al. 2010 [1]_).
 
 This document also provides `Detailed instructions for using DART and CESM POP2
-on NCAR's supercomputer`_, including information about the availability of
+on NSF NCAR's supercomputer`_, including information about the availability of
 restart files for `Creating an initial ensemble`_ of model states and
 `Observation sequence files`_ for assimilation.
 
@@ -30,7 +30,7 @@ In years subsequent to the initial development of the DART interface, the
 Computer, Computational, and Statistical Sciences Division at LANL transitioned
 from using POP as their primary ocean model to using the Model for Prediction
 Across Scales-Ocean (MPAS-Ocean). Thus it became difficult for staff in the
-Data Assimilation Research Section (DAReS) at NCAR to maintain access to the
+Data Assimilation Research Section (DAReS) at NSF NCAR to maintain access to the
 `LANL POP <https://climatemodeling.science.energy.gov/projects/climate-ocean-and-sea-ice-modeling-cosim>`_
 source code. As a result, LANL POP has been tested using DART's Lanai framework
 but has not been tested using DART's Manhattan framework. If you intend to use
@@ -40,10 +40,10 @@ [email protected].
 CESM POP2
 ~~~~~~~~~
 
-The NCAR implementation of POP, `CESM POP2
+The NSF NCAR implementation of POP, `CESM POP2
 <https://ncar.github.io/POP/doc/build/html/index.html>`_, has been used
-extensively with DART throughout multiple generations of NCAR's supercomputer 
-(Bluefire, Yellowstone & Cheyenne) and multiple iterations of NCAR's earth
+extensively with DART throughout multiple generations of NSF NCAR's supercomputer 
+(Bluefire, Yellowstone & Cheyenne) and multiple iterations of NSF NCAR's earth
 system model (CCSM4, CESM1 and CESM2). CESM POP2 is supported under DART's
 Manhattan framework.
 
@@ -52,24 +52,24 @@ to manage the ensemble and the Flux Coupler is responsible for stopping POP2 at
 the times required to perform an assimilation. CESM runs continuously and all
 of the DART routines run at each assimilation time.
 
-Detailed instructions for using DART and CESM POP2 on NCAR's supercomputer
---------------------------------------------------------------------------
+Detailed instructions for using DART and CESM POP2 on NSF NCAR's supercomputer
+------------------------------------------------------------------------------
 
-If you're using NCAR's supercomputer, you can run the setup scripts after
+If you're using NSF NCAR's supercomputer, you can run the setup scripts after
 making minor edits to set details that are specific to your project. The setup
 scripts create a CESM case in which POP is configured using a 1° horizontal
 grid, and uses the eddy parametrization of  Gent and McWilliams (1990). [2]_
 The CICE model is active and atmospheric forcing is provided by the `CAM6 DART
 Reanalysis <https://rda.ucar.edu/datasets/ds345.0/>`_.
 
-The filesystem attached to NCAR's supercomputer is known as the Globally
+The filesystem attached to NSF NCAR's supercomputer is known as the Globally
 Accessible Data Environment (GLADE). All filepaths on GLADE have the structure:
 
 .. code-block::
 
    /glade/*
 
-If you aren't using NCAR's supercomputer, take note of when the ``/glade/``
+If you aren't using NSF NCAR's supercomputer, take note of when the ``/glade/``
 filepath is present in the setup scripts, since this will indicate sections
 that you must alter in order to get the scripts to work on your supercomputer.
 Additionally, you'll need to generate your own initial condition and
@@ -80,7 +80,7 @@ staff by emailing [email protected] for assistance.
 Summary
 -------
 
-To use DART and CESM POP2 on NCAR's supercomputer, you will need to complete
+To use DART and CESM POP2 on NSF NCAR's supercomputer, you will need to complete
 the following steps.
 
 #. Configure the scripts for your specific experiment by editing
@@ -134,8 +134,8 @@ access to this directory by CISL. Use the `Service Desk
 you're unable to get permission, contact DAReS staff for assistance by emailing
 [email protected].
 
-Filepaths beginning with ``/glade/campaign/*`` can't be accessed from NCAR's 
-supercomputer nodes. You must log on to NCAR's data visualization computer to
+Filepaths beginning with ``/glade/campaign/*`` can't be accessed from NSF NCAR's 
+supercomputer nodes. You must log on to NSF NCAR's data visualization computer to
 copy files from ``/glade/campaign/*``.
 
 This python script was created by *Dan Amrhein*. Thanks Dan!
@@ -147,13 +147,13 @@ This python script was created by *Dan Amrhein*. Thanks Dan!
 |                               | g210.G_JRA.v14.gx1v7.01 experiment that are saved in      |
 |                               | campaign storage. You must be granted access to the CGD   |
 |                               | Ocean Section campaign storage directory and be logged on |
-|                               | to NCAR's data visualization computer in order to run     |
+|                               | to NSF NCAR's data visualization computer in order to run |
 |                               | this script. The assignment of the ``stagedir`` variable  |
 |                               | in this script should match the assignment of the         |
 |                               | ``stagedir`` variable in ``DART_params.csh``.             |
 +-------------------------------+-----------------------------------------------------------+
 
-In order to use this script, log in to NCAR's data visualization computer and
+In order to use this script, log in to NSF NCAR's data visualization computer and
 use python to run the script. For example:
 
 .. code-block::
@@ -420,7 +420,7 @@ References
 
 .. [1] Smith, R., and Coauthors, 2010: The Parallel Ocean Program (POP)
        Reference Manual Ocean Component of the Community Climate System Model
-       (CCSM) and Community Earth System Model (CESM). National Center for
+       (CCSM) and Community Earth System Model (CESM). NSF National Center for
        Atmospheric Research,
        `http://www.cesm.ucar.edu/ models/cesm1.0/pop2/doc/sci/POPRefManual.pdf <http://www.cesm.ucar.edu/ models/cesm1.0/pop2/doc/sci/POPRefManual.pdf>`_.
 

models/cam-fv/readme.rst

@@ -21,7 +21,7 @@ An interface to MPAS is being developed (contact us about the current status).
 The flexibility of the DART environment has led to its use
 by graduate students, post-graduates, and scientists at universities and
 research labs to conduct data assimilation research. Others are using the
-products of data assimilation (analyses), which were produced here at NCAR
+products of data assimilation (analyses), which were produced at NSF NCAR
 using CESM+DART, to conduct related research. 
 The latest reanalysis is described in the DART |CAM6_Rean|_
 
@@ -117,14 +117,14 @@ Reanalyses
 
 There have been two large-scale reanalysis efforts using CAM-FV and DART. 
 The **CAM6 Data Assimilation Research Testbed (DART) Reanalysis**
-is archived in the NCAR Research Data Archive 
+is archived in the NSF NCAR Research Data Archive 
 `DS345.0 <https://rda.ucar.edu/datasets/ds345.0/#!description>`__ .
 (See the |CAM6_Rean|_ ).
 It contains just under 120Tb (yes Tb) of data:
 
    These CAM6+DART Reanalysis data 
    products are designed to facilitate a broad variety of research using 
-   NCAR's CESM2 models, ranging from model evaluation to (ensemble) 
+   NSF NCAR's CESM2 models, ranging from model evaluation to (ensemble) 
    hindcasting (initial conditions), data assimilation experiments, and sensitivity studies. 
    They come from an 80 member ensemble reanalysis of the global 
    troposphere and stratosphere using CAM6-FV from CESM2.1. 
@@ -138,7 +138,7 @@ It contains just under 120Tb (yes Tb) of data:
 An earlier, more limited dataset can be found in the 
 `**Ensemble of Atmospheric Forcing Files from a CAM4-FV Reanalysis** 
 <https://github.com/NCAR/DART/wiki/2-degree-DATM-ensemble-for-CESM-experiments-(1998-thru-2010)>`__
-is archived in the NCAR Research Data Archive 
+is archived in the NSF NCAR Research Data Archive 
 `DS199.1 <https://rda.ucar.edu/datasets/ds199.1/>`__ .
 It contains about 1.5Tb of data:
 
@@ -147,7 +147,7 @@ It contains about 1.5Tb of data:
    Research Testbed (DART) using the Community Atmosphere Model Version 
    4 with the finite volume core (CAM4-FV) at 1.9 degree by 2.5 degree 
    resolution. The observations assimilated include all those used in 
-   the NCEP/NCAR reanalysis (temperature and wind components from 
+   the NCEP/NSF NCAR reanalysis (temperature and wind components from 
    radiosondes, aircraft, and satellite drift winds) plus radio 
    occultation observations from the COSMIC satellites starting in late 
    2006. These files are intended to be used as 'DATM stream files' 
@@ -164,13 +164,13 @@ The CAM6+DART Reanalysis used "observation sequence files"
 which contain the types of observations in the table below
 ("T" = temperature, "U" = zonal wind, "V" = meridional wind,
 "Q" = specific humidity, "refractivity" = the bending of light by density variations).
-These files are available on NCAR's glade file system:
+These files are available on NSF NCAR's glade file system:
 /glade/p/cisl/dares/Observations/NCEP+ACARS+GPS+AIRS/Thinned_x9x10.
 Versions of these files, which also have the results of the reanalysis in them,
 are available from the RDA ds345.0 linked above.
 
 NCEP
-   NCEP's PREPBUFR files (prepqm) in NCAR's Research Data Archive:
+   NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive:
    (https://rda.ucar.edu/datasets/ds090.0/)
 
 COSMIC