Merge pull request #62 from kayeekayee/2024aug4_be0410e

Update to hash #be0410e (Apr 23)

.github/workflows/gcc.yml

@@ -9,7 +9,7 @@ defaults:
     shell: bash -leo pipefail {0}
 
 env:
-  cache_key: gcc2  # The number (#) following the cache_key "gcc" is to flush Action cache.
+  cache_key: gcc3  # The number (#) following the cache_key "gcc" is to flush Action cache.
   CC: gcc-10
   FC: gfortran-10
   CXX: g++-10
@@ -60,6 +60,7 @@ jobs:
           sudo apt install cmake
           spack external find
           spack add [email protected]
+          spack add doxygen
           spack concretize
           spack install -v --fail-fast --dirty
           spack clean --all
@@ -91,6 +92,6 @@ jobs:
           export FC=mpif90
           cd UPP
           mkdir -p build && cd build
-          cmake -DCMAKE_INSTALL_PREFIX=../install ..
+          cmake -DENABLE_DOCS=ON -DCMAKE_INSTALL_PREFIX=../install ..
           make -j2 VERBOSE=1
           make install

.github/workflows/intel.yml

@@ -59,7 +59,7 @@ 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

.gitignore

@@ -9,7 +9,7 @@
 # USE CAUTION WHEN ADDING WILDCARDS, as some builds use different filename   #
 # conventions than others                                                    #
 ##############################################################################
-build*/
+build/*/
 install*/
 
 *.[aox]

.readthedocs.yml

@@ -11,7 +11,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: doc/UserGuide/conf.py
 
 # Build documentation with MkDocs
 #mkdocs:
@@ -22,6 +22,5 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-#  version: 3.7
   install:
-    - requirements: docs/requirements.txt
+    - requirements: doc/UserGuide/requirements.txt

CMakeLists.txt

@@ -14,6 +14,7 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 # Handle user options.
 option(OPENMP "use OpenMP threading" ON)
 option(BUILD_POSTEXEC "Build NCEPpost executable" ON)
+option(BUILD_WITH_NEMSIO "Build NCEPpost with nemsio library" ON)
 option(BUILD_WITH_WRFIO "Build NCEPpost with WRF-IO library" OFF)
 option(BUILD_WITH_IFI "Build NCEPpost with In-Flight Icing (IFI) library if present" OFF)
 option(REQUIRE_IFI "Abort if libIFI is not found ; enables BUILD_WITH_IFI=ON" OFF)
@@ -84,9 +85,10 @@ else()
 endif()
 
 if(BUILD_POSTEXEC)
-  find_package(nemsio REQUIRED)
-  find_package(sfcio REQUIRED)
-  find_package(sigio REQUIRED)
+  if(BUILD_WITH_NEMSIO)
+    find_package(nemsio REQUIRED)
+    find_package(sigio REQUIRED)
+  endif()
   find_package(sp REQUIRED)
   find_package(w3emc REQUIRED)
   if(BUILD_WITH_WRFIO)
@@ -116,7 +118,7 @@ add_subdirectory(parm)
 # If desired, build the doxygen docs.
 if(ENABLE_DOCS)
   find_package(Doxygen REQUIRED)
-  add_subdirectory(docs)
+  add_subdirectory(doc)
 endif()
 
 ### Package config

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:
@@ -48,26 +47,24 @@ 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 NCEPLIBS packages to be installed via the 
-HPC-Stack project. For instructions on installing these packages as a 
-bundle via HPC-Stack, see: https://hpc-stack.readthedocs.io/en/latest/.
-Users may instead install packages via spack-stack. For instructions,
-see: https://spack-stack.readthedocs.io/en/latest/.
+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. 
 
@@ -87,7 +84,6 @@ 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
@@ -110,7 +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.