Merge remote-tracking branch 'upstream/develop' into develop

.github/workflows/intel.yml

@@ -9,7 +9,7 @@ defaults:
 
 # Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
 env:
-  cache_key: intel2  # The number (#) following the cache_key "intel" is to flush Action cache.
+  cache_key: intel3  # The number (#) following the cache_key "intel" is to flush Action cache.
   CC: icc
   FC: ifort
   CXX: icpc
@@ -33,7 +33,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
       - name: checkout-upp  # This is for getting spack.yaml
@@ -45,7 +45,7 @@ jobs:
       # Cache spack, compiler and dependencies
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
@@ -59,14 +59,13 @@ jobs:
           sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
           sudo apt-get update
-          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran-2023.2.1 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.1
           echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
 
       # Install dependencies using Spack
       - name: install-dependencies-with-spack
         if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
-          sudo mv /usr/local/ /usr_local_mv
           git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
           source spack/share/spack/setup-env.sh
           spack env create upp-env UPP/ci/spack.yaml
@@ -81,7 +80,7 @@ jobs:
 
   build:
     needs: setup
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
       - name: checkout-upp
@@ -95,7 +94,7 @@ jobs:
 
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack

.readthedocs.yml

@@ -4,10 +4,14 @@
 
 # Required
 version: 2
+build: 
+  os: ubuntu-20.04
+  tools: 
+    python: "3.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: docs/UserGuide/conf.py
 
 # Build documentation with MkDocs
 #mkdocs:
@@ -17,8 +21,7 @@ sphinx:
 formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
-#python:
+python:
 #  version: 3.7
-#  install:
-
-#    - requirements: docs/requirements.txt
+  install:
+    - requirements: docs/UserGuide/requirements.txt

README.md

@@ -1,33 +1,32 @@
 
-# Unified Post-Processing (UPP)
+# Unified Post Processor (UPP)
 
 The Unified Post Processor (UPP) software package is a software
 package designed to generate useful products from raw model
 output.
 
 The UPP is currently used in operations with the Global Forecast
 System (GFS), GFS Ensemble Forecast System (GEFS), North American
-Mesoscale (NAM), Rapid Refresh (RAP), High Resolution Rapid Refresh
+Mesoscale (NAM), Rapid Refresh (RAP), High-Resolution Rapid Refresh
 (HRRR), Short Range Ensemble Forecast (SREF), and Hurricane WRF (HWRF)
-applications. It is also used in the Unified Forecasting System (UFS),
-including the Rapid Refresh Forecast System (RRFS), Hurricane Application
-Forecasting System (HAFS), and the Medium Range Weather (MRW) and Short 
+applications. It is also used in the Unified Forecast System (UFS),
+including the Rapid Refresh Forecast System (RRFS), Hurricane Analysis and
+Forecast System (HAFS), and the Medium-Range Weather (MRW) and Short-
 Range Weather (SRW) Applications.
 
 The UPP provides the capability to compute a variety of diagnostic
 fields and interpolate to pressure levels or other vertical
 coordinates.
 
 UPP also incorporates the Joint Center for Satellite Data Assimilation
-(JCSDA) Community Radiative Transfer Model (CRTM) to compute model
-derived brightness temperature (TB) for various instruments and
+(JCSDA) Community Radiative Transfer Model (CRTM) to compute model-derived brightness temperature (TB) for various instruments and
 channels. This additional feature enables the generation of a number
 of simulated satellite products including GOES products.
 
 Output from the UPP is in National Weather Service (NWS) and World
 Meteorological Organization (WMO) GRIB2 format and can be used
-directly by visualization, plotting, or verification packages, or for
-further downstream post-processing, e.g. statistical post-processing
+directly by visualization, plotting, or verification packages or for
+further downstream post-processing, e.g., statistical post-processing
 techniques.
 
 Examples of UPP products include:
@@ -48,31 +47,35 @@ Examples of UPP products include:
 Support for the UFS UPP is provided through [GitHub Discussions](https://github.com/NOAA-EMC/UPP/discussions).
 
 ## Documentation 
-User Guide for latest public release: https://upp.readthedocs.io/en/latest/.
+User Guide for latest standalone public release: https://upp.readthedocs.io/en/latest/.
 
 Technical code-level documentation: https://noaa-emc.github.io/UPP/.
 
 ## Developer Information
-Please see review the [wiki](https://github.com/NOAA-EMC/UPP/wiki)
+Please review the [wiki](https://github.com/NOAA-EMC/UPP/wiki)
 
 ## Authors
 
 NCEP/EMC Developers
 
-Code Managers: Wen Meng, Huiya Chuang, Kate Fossell
+Code Managers: Wen Meng, Huiya Chuang, Fernando Andrade-Maldonado
 
 ## Prerequisites
 
-The UPP requires certain NCEPLIB packages to be installed via
-the HPC-Stack project.  
+The UPP requires certain NCEPLIBS packages to be installed via the 
+spack-stack project. For instructions on installing these packages as a 
+bundle via spack-stack, see: https://spack-stack.readthedocs.io/en/latest/.
+The `UPP/modulefiles` directory indicates which package versions are 
+used and supported on Level 1 systems. 
+
+Required NCEPLIBS packages:
 
 - [NCEPLIBS-g2](https://github.com/NOAA-EMC/NCEPLIBS-g2)
 - [NCEPLIBS-g2tmpl](https://github.com/NOAA-EMC/NCEPLIBS-g2tmpl)
 - [NCEPLIBS-sp](https://github.com/NOAA-EMC/NCEPLIBS-sp)
 - [NCEPLIBS-ip](https://github.com/NOAA-EMC/NCEPLIBS-ip)
 - [NCEPLIBS-bacio](https://github.com/NOAA-EMC/NCEPLIBS-bacio)
 - [NCEPLIBS-w3emc](https://github.com/NOAA-EMC/NCEPLIBS-w3emc)
-- [NCEPLIBS-w3nco](https://github.com/NOAA-EMC/NCEPLIBS-w3nco)
 - [CRTM](https://github.com/noaa-emc/emc_crtm)
 
 Also required to build NCEPpost executable (cmake option
@@ -81,19 +84,20 @@ BUILD_POSTEXEC):
 - [NCEPLIBS-sigio](https://github.com/NOAA-EMC/NCEPLIBS-sigio)
 - [NCEPLIBS-sfcio](https://github.com/NOAA-EMC/NCEPLIBS-sfcio)
 - [NCEPLIBS-nemsio](https://github.com/NOAA-EMC/NCEPLIBS-nemsio)
-- [NCEPLIBS-gfsio](https://github.com/NOAA-EMC/NCEPLIBS-gfsio)
 
 The [NCEPLIBS-wrf_io](https://github.com/NOAA-EMC/NCEPLIBS-wrf_io)
 library is required to build with NCEPpost with WRF-IO library (cmake
 option BUILD_WITH_WRFIO).
 
 The following third-party libraries are required:
 
+- [netcdf](https://github.com/Unidata/netcdf)
 - [netcdf-c](https://github.com/Unidata/netcdf-c)
 - [netcdf-fortran](https://github.com/Unidata/netcdf-fortran)
 - [Jasper](https://github.com/jasper-software/jasper)
 - [libpng](http://www.libpng.org/pub/png/libpng.html)
-- [libz](https://zlib.net/)
+- [zlib](https://zlib.net/)
+- [hdf5](https://github.com/HDFGroup/hdf5)
 
 ## Building
 
@@ -102,7 +106,7 @@ Builds include:
 - Inline post (UPP library): Currently only supported for the GFS, RRFS,
   HAFS, and the UFS-MRW Application.
 
-- Offline post (UPP executable): Supported for Regional applications
+- Offline post (UPP executable): Supported for regional applications
   including SRW, RRFS, HAFS, and standalone applications of UPP.
 
 
@@ -128,3 +132,7 @@ Commerce. The Department of Commerce seal and logo, or the seal and
 logo of a DOC bureau, shall not be used in any manner to imply
 endorsement of any commercial product or activity by DOC or the United
 States Government.
+
+## UPP Terms of Use Notice
+
+The UPP Terms of Use Notice is available at: https://github.com/NOAA-EMC/UPP/wiki/UPP-Terms-of-Use-Notice