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

.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 mpich@3.4.2
+          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

.gitignore

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

.readthedocs.yml

@@ -11,7 +11,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/UserGuide/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/UserGuide/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)
@@ -111,12 +113,11 @@ if(IFI_FOUND OR INTERNAL_IFI)
 endif()
 
 add_subdirectory(sorc)
-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

ci/rt.sh

@@ -4,9 +4,11 @@
 # Wen Meng, 12/2020, First version.
 # Fernando Andrade-Maldonado 5/2023 rework for CLI Options
 # Fernando Andrade-Maldonado / Wen Meng 9/2023 Add Hercules, fix typos, and refactor
-#
+# Fernando Andrade-Maldonado 4/2024 Additional Log info
 ######################################################################
 
+SECONDS=0
+
 git_branch="develop"
 git_url="https://github.com/NOAA-EMC/UPP.git"
 clone_on="no"
@@ -65,26 +67,28 @@ if [ $mac2 = hf ]; then # for HERA
  export machine=HERA
  export homedir=${homedir:-"/scratch2/NAGAPE/epic/UPP/test_suite"}
  export rundir=${rundir:-"/scratch1/NCEPDEV/stmp2/${USER}"}
- module use /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core
+ module use /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core
  module load stack-intel/2021.5.0
  module load stack-intel-oneapi-mpi/2021.5.1
  module load prod_util/2.1.1
-elif [ $mac = O ] ; then
+elif [ $mac3 = orio ] ; then
  export machine=ORION
  export homedir=${homedir:-"/work/noaa/epic/UPP"}
  export rundir=${rundir:-"/work2/noaa/stmp/$USER"}
- module use /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core
- module load stack-intel/2022.0.2
- module load stack-intel-oneapi-mpi/2021.5.1
+ module use /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core
+ module load stack-intel/2021.9.0
+ module load stack-intel-oneapi-mpi/2021.9.0
  module load prod_util/2.1.1
+ module load python/3.10.8
 elif [ $mac3 = herc ] ; then
  export machine=HERCULES
  export homedir=${homedir:-"/work/noaa/epic/UPP"}
  export rundir=${rundir:-"/work2/noaa/stmp/$USER"}
- module use /work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core
+ module use /work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core
  module load stack-intel/2021.9.0
  module load stack-intel-oneapi-mpi/2021.9.0
  module load prod_util/2.1.1
+ module load python/3.10.8
 fi
 
 #set working directory
@@ -235,17 +239,42 @@ for job_id in $jobid_list; do
   fi
 done
 
+elapsed_time=$( printf '%02dh:%02dm:%02ds\n' $((SECONDS%86400/3600)) $((SECONDS%3600/60)) $((SECONDS%60)) )
+
 python ${test_v}/ci/rt-status.py
 test_results=$?
 
 # Cleanup rt log
+cd ${test_v}
+
+UPP_HASH=$(git rev-parse HEAD)
+SUBMODULE_HASHES=$(git submodule status --recursive)
+DATE="$(date '+%Y%m%d %T')"
+
 cd ${test_v}/ci
-echo "rundir: ${rundir}" > rt.log.${machine}.temp
+
+cat << EOF > rt.log.${machine}.temp
+===== Start of UPP Regression Testing Log =====
+UPP Hash Tested:
+${UPP_HASH}
+
+Submodule hashes:
+${SUBMODULE_HASHES}
+
+Run directory: ${rundir}
+Baseline directory: ${homedir}
+
+Total runtime: ${elapsed_time}
+Test Date: ${DATE}
+Summary Results:
+
+EOF
+
 cat rt.log.${machine} | grep "test:" >> rt.log.${machine}.temp
 cat rt.log.${machine} | grep "baseline" >> rt.log.${machine}.temp
 python ${test_v}/ci/rt-status.py >> rt.log.${machine}.temp
-cat rt.log.${machine}.temp > rt.log.${machine}
-rm rt.log.${machine}.temp
+echo "===== End of UPP Regression Testing Log =====" >> rt.log.${machine}.temp
+mv rt.log.${machine}.temp rt.log.${machine}
 mv rt.log.${machine} ${test_v}/tests/logs
 
 # should indicate failure to Jenkins

ci/spack.yaml

@@ -11,7 +11,7 @@ spack:
   - bacio@2.4.1
   - w3emc@2.10.0
   - g2@3.4.5
-  - g2tmpl@1.10.2
+  - g2tmpl@1.12.0
   - sp@2.5.0
   - ip@4.3.0
   - sigio@2.3.2