Merge branch 'ufs-community:develop' into feature/gaea-c5

.github/workflows/aux.yml

@@ -1,9 +1,12 @@
-name: Helpers
+name: Repo Check
 on:
-  workflow_run:
-    workflows: ["Pull Request Tests"]
-    types:
-      - requested
+  #workflow_run:
+  #  workflows: ["Pull Request Tests"]
+  #  types:
+  #    - requested
+  pull_request:
+    branches:
+      - develop
 env:
   app: Accept:application/vnd.github.v3+json
   base_url: $GITHUB_API_URL/repos/$GITHUB_REPOSITORY/actions/runs
@@ -30,24 +33,28 @@ jobs:
     steps:
     - name: Check up-to-dateness and post comment
       run: |
-        head_sha=${{ github.event.workflow_run.head_sha }}
-        git clone -q ${{ github.event.workflow_run.head_repository.html_url }} .
+        trap 'echo "exit-code=$?" >> "$GITHUB_OUTPUT"' EXIT
+        head_sha=${{ github.event.pull_request.head.sha }}
+        head_brc=${{ github.event.pull_request.head.ref }}
+        head_url=${{ github.event.pull_request.head.repo.html_url }}
+        git clone -q -b $head_brc $head_url .
         git checkout -q $head_sha
         git submodule -q update --init --recursive
         cd ${{ github.workspace }}/tests/ci
         url=$GITHUB_API_URL/repos/$GITHUB_REPOSITORY
         pr_number=$(curl -sS -H $app $url/pulls \
           | jq -r '.[] | select(.head.sha == "'"$head_sha"'") | .number')
         echo "pr_number is $pr_number"
-        pr_uid=${{ github.event.workflow_run.head_repository.owner.login }}
+        pr_uid=${{ github.event.pull_request.head.repo.owner.login }}
         echo "pr_uid is $pr_uid"
-        comment="$(./repo_check.sh $pr_uid 2>/dev/null)"
-        echo "comment is $comment"
-        if [[ -n $comment ]]; then
-          curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-            $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
-          echo -n "failure" >~/repocheck_file
-        else
-          echo -n "success" >~/repocheck_file
-        fi
+        ./repo_check.sh
+        #comment="$(./repo_check.sh 2>/dev/null)"
+        #echo "comment is $comment"
+        #if [[ -n $comment ]]; then
+        #  curl -sS -X POST -H $app -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+        #    $url/issues/$pr_number/comments -d '{"body": "'"${comment}"'"}'
+        #  echo -n "failure" >~/repocheck_file
+        #else
+        #  echo -n "success" >~/repocheck_file
+        #fi
         

.github/workflows/superlinter.yml

@@ -0,0 +1,37 @@
+---
+name: Super-Linter
+
+on:
+  push: null
+  pull_request: null
+
+jobs:
+  build:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: read
+      statuses: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Super-Linter
+        uses: super-linter/[email protected]
+        env:
+          LINTER_RULES_PATH: /
+          DEFAULT_BRANCH: origin/develop
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          FILTER_REGEX_EXCLUDE: .*(tests/fv3_conf/.*|tests/ci/.*|tests/auto/.*|tests/auto-jenkins/.*|tests/opnReqTests/.*|tests/opnReqTest|tests/atparse.bash).*
+          VALIDATE_BASH: true
+          BASH_SEVERITY: style
+          #VALIDATE_GITHUB_ACTIONS: true
+          #VALIDATE_LUA: true
+          #VALIDATE_MARKDOWN: true
+          #VALIDATE_PYTHON_PYLINT: true
+          #VALIDATE_YAML: true

.shellcheckrc

@@ -0,0 +1,16 @@
+# Global settings for Shellcheck (https://github.com/koalaman/shellcheck)
+enable=all
+
+external-sources=true
+
+# Disable variable referenced but not assigned
+disable=SC2154
+
+# Disable following non-constant source
+disable=SC1090
+
+# Disable non-existent binary
+disable=SC1091
+
+# Disable -p -m only applies to deepest directory
+disable=SC2174

CICE-interface/CMakeLists.txt

@@ -39,7 +39,7 @@ else()
 endif()
 
 # Configuration Options
-set(CICE_IO "NetCDF" CACHE STRING "CICE OPTIONS: Choose IO options.")
+set(CICE_IO "PIO" CACHE STRING "CICE OPTIONS: Choose IO options.")
 set_property(CACHE CICE_IO PROPERTY STRINGS "NetCDF" "PIO" "Binary")
 
 # Too many files to list, so include them via this file

CMakeLists.txt

@@ -73,6 +73,7 @@ set(JEDI_DRIVER     OFF CACHE BOOL "Enable JEDI as top level driver")
 set(CMEPS_AOFLUX    OFF CACHE BOOL "Enable atmosphere-ocean flux calculation in mediator")
 set(PDLIB           OFF CACHE BOOL "Enable Domain Decomposition in WW3 via PDLIB")
 set(CDEPS_INLINE    OFF CACHE BOOL "Enable CDEPS inline capability")
+set(HYDRO           OFF CACHE BOOL "Enable hydrostatic set")
 
 set(CMAKE_Platform $ENV{CMAKE_Platform})
 if(CMAKE_Platform)
@@ -122,6 +123,7 @@ message("PARALLEL_NETCDF .. ${PARALLEL_NETCDF}")
 message("JEDI_DRIVER ...... ${JEDI_DRIVER}")
 message("CMEPS_AOFLUX ..... ${CMEPS_AOFLUX}")
 message("CDEPS_INLINE ..... ${CDEPS_INLINE}")
+message("HYDRO  ........... ${HYDRO}")
 
 message("")
 

NOAHMP-interface/CMakeLists.txt

@@ -8,9 +8,10 @@ list(APPEND _noahmp_cap_files noahmp/drivers/nuopc/lnd_comp_kind.F90
                               noahmp/drivers/nuopc/lnd_comp_domain.F90
                               noahmp/drivers/nuopc/lnd_comp_import_export.F90
                               noahmp/drivers/nuopc/lnd_comp_nuopc.F90
-                              noahmp/drivers/nuopc/lnd_comp_driver.F90)
+                              noahmp/drivers/nuopc/lnd_comp_driver.F90
+			      noahmp/drivers/nuopc/lnd_comp_cplscalars.F90)
 
-# CCPP interface 
+# CCPP interface
 list(APPEND _noahmp_ccpp_files noahmp/drivers/ccpp/noahmpdrv.F90
                                noahmp/drivers/ccpp/sfc_diff.f
                                noahmp/drivers/ccpp/machine.F
@@ -25,7 +26,7 @@ list(APPEND _noahmp_files noahmp/src/module_sf_noahmplsm.F90
                           noahmp/src/module_sf_noahmp_glacier.F90)
 
 #------------------------------------------------------------------------------
-# Set CCPP flags for C/C++/Fortran preprocessor 
+# Set CCPP flags for C/C++/Fortran preprocessor
 add_definitions(-DCCPP)
 
 #------------------------------------------------------------------------------
@@ -55,8 +56,10 @@ endif()
 
 #------------------------------------------------------------------------------
 # Add model-specific flags for C/C++/Fortran preprocessor
-add_definitions(-DMOIST_CAPPA -DUSE_COND -DNEMS_GSM)
-add_definitions(-DINTERNAL_FILE_NML)
+if (NOT HYDRO)
+add_definitions(-DMOIST_CAPPA -DUSE_COND)
+endif()
+add_definitions(-DINTERNAL_FILE_NML -DNEMS_GSM)
 
 #------------------------------------------------------------------------------
 # NOAHMP

build.sh

@@ -1,21 +1,29 @@
 #!/bin/bash
 set -eu
-
-if [[ $(uname -s) == Darwin ]]; then
-  readonly UFS_MODEL_DIR=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+uname_s=$(uname -s)
+if [[ ${uname_s} == Darwin ]]; then
+  UFS_MODEL_DIR=$(greadlink -f -n "${BASH_SOURCE[0]}")
+  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
+  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
 else
-  readonly UFS_MODEL_DIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
+  UFS_MODEL_DIR=$(readlink -f -n "${BASH_SOURCE[0]}")
+  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
+  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
 fi
+echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
+readonly UFS_MODEL_DIR
 
 export CC=${CC:-mpicc}
 export CXX=${CXX:-mpicxx}
 export FC=${FC:-mpif90}
 
 BUILD_DIR=${BUILD_DIR:-${UFS_MODEL_DIR}/build}
-mkdir -p ${BUILD_DIR}
+mkdir -p "${BUILD_DIR}"
 
-cd ${BUILD_DIR}
-cmake ${UFS_MODEL_DIR} ${CMAKE_FLAGS}
+cd "${BUILD_DIR}"
+ARR_CMAKE_FLAGS=()
+for i in ${CMAKE_FLAGS}; do ARR_CMAKE_FLAGS+=("${i}") ; done
+cmake "${UFS_MODEL_DIR}" "${ARR_CMAKE_FLAGS[@]}"
 # Turn off OpenMP threading for parallel builds
 # to avoid exhausting the number of user processes
-OMP_NUM_THREADS=1 make -j ${BUILD_JOBS:-4} VERBOSE=${BUILD_VERBOSE:-}
+OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-}"

cmake/Intel.cmake

@@ -1,6 +1,15 @@
-set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -nowarn -sox -align array64byte -qno-opt-dynamic-align")
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback -fpp -fno-alias -auto -safe-cray-ptr -ftz -assume byterecl -sox -align array64byte -qno-opt-dynamic-align")
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qno-opt-dynamic-align -sox -fp-model source")
 
+# warning #5462: Global name too long.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 5462")
+
+# remark #7712: This variable has not been used.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 7712")
+
+# remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -diag-disable 8291")
+
 if(CMAKE_Platform STREQUAL "derecho.intel")
   set(CMAKE_Fortran_LINK_FLAGS "-Wl,--copy-dt-needed-entries")
 endif()

doc/UsersGuide/requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 #    pip-compile requirements.in
@@ -12,21 +12,19 @@ certifi==2024.2.2
     # via requests
 charset-normalizer==3.3.2
     # via requests
+colorama==0.4.6
+    # via sphinx
 docutils==0.20.1
     # via
     #   pybtex-docutils
     #   sphinx
     #   sphinx-rtd-theme
     #   sphinxcontrib-bibtex
-idna==3.6
+idna==3.7
     # via requests
 imagesize==1.4.1
     # via sphinx
-importlib-metadata==7.0.1
-    # via
-    #   sphinx
-    #   sphinxcontrib-bibtex
-jinja2==3.1.3
+jinja2==3.1.4
     # via sphinx
 latexcodec==2.0.1
     # via pybtex
@@ -44,7 +42,7 @@ pygments==2.17.2
     # via sphinx
 pyyaml==6.0.1
     # via pybtex
-requests==2.31.0
+requests==2.32.0
     # via sphinx
 six==1.16.0
     # via
@@ -78,5 +76,3 @@ sphinxcontrib-serializinghtml==1.1.10
     # via sphinx
 urllib3==2.2.1
     # via requests
-zipp==3.17.0
-    # via importlib-metadata

doc/UsersGuide/source/BuildingAndRunning.rst

@@ -582,7 +582,9 @@ To run a single test, users can try the following command instead of creating a
 
 .. code-block:: console
 
-   ./rt.sh -r -k -n control_p8
+   ./rt.sh -r -k -n "control_p8 <compiler>"
+
+where ``<compiler>`` is ``gnu`` or ``intel``. 
 
 Troubleshooting
 ^^^^^^^^^^^^^^^^^^