generalization of number of soil layers

.github/pull_request_template.md

@@ -1,83 +1,153 @@
-## Description
+<!-- INSTRUCTIONS: 
+- PLEASE READ/FOLLOW THE DIRECTIONS IN EACH SECTION
+- Complete the 'Commit Queue Requirements' below
+- Please use github markup as much as possible (https://docs.github.com/en/get-started/writing-on-github)
+- Please leave your PR in a draft state until all underlying work is completed.
+-->
+## Commit Queue Requirements:
+<!--
+- Please complete the items that follow this.
+- Please "check off" completed items. Use [X] for a filled in checkbox or leave it [ ] for an empty checkbox
+- Your PR will not be considered until all requirements are met.
+- THIS IS YOUR RESPONSIBILITY
+ -->
+- [ ] Fill out all sections of this template.
+- [ ] All sub component pull requests have been reviewed by their code managers.
+- [ ] Run the full Intel+GNU RT suite (compared to current baselines) on either Hera/Derecho/Hercules
+- [ ] Commit 'test_changes.list' from previous step
+---
+## Description:
 <!--
-Provide a detailed description of what this PR does. What bug does it fix, or what feature does it add? Is a change of answers expected from this PR? Are any library updates included in this PR (modulefiles etc.)?
+Please provide a detailed verbose description of what this PR does
 -->
 
-### Input data additions/changes
-- [ ] No changes are expected to input data.
-- [ ] Changes are expected to input data:
-  - [ ] New input data.
-  - [ ] Updated input data.
-
-### Anticipated changes to regression tests:
-- [ ] No changes are expected to any regression test.
-- [ ] Changes are expected to the following tests:
-<!-- Please insert what RT's change and why you expect them to change -->
-
-## Subcomponents involved:
-- [ ] AQM
-- [ ] CDEPS
-- [ ] CICE
-- [ ] CMEPS
-- [ ] CMakeModules
-- [ ] FV3
-- [ ] GOCART
-- [ ] HYCOM
-- [ ] MOM6
-- [ ] NOAHMP
-- [ ] WW3
-- [ ] stochastic_physics
-- [ ] none
 
-### Library Updates/Changes
-<!-- Library updates take time. If this PR needs updates to libraries, please make sure to accomplish the following tasks -->
-- [ ] Not Needed
-- [ ] Create separate issue in [JCSDA/spack-stack](https://github.com/JCSDA/spack-stack) asking for update to library. Include library name, library version.
-- [ ] Add issue link from JCSDA/spack-stack following this item
-<!-- for example: "- JCSDA/spack-stack/issue/1757" -->
+### Commit Message:
+<!--
+Please provide concise information for The UFS-WM and/or each sub-component:
+Please delete what is not needed.
+-->
+```
+* UFSWM - 
+  * AQM - 
+  * CDEPS - 
+  * CICE - 
+  * CMEPS - 
+  * CMakeModules - 
+  * FV3 - 
+    * ccpp-physics - 
+    * atmos_cubed_sphere - 
+  * GOCART - 
+  * HYCOM - 
+  * MOM6 - 
+  * NOAHMP - 
+  * WW3 - 
+  * stochastic_physics - 
+```
 
-### Combined with PR's (If Applicable):
+### Priority:
+<!--
+Please provide the priority you would prefer this pull request to have.
+* Critical Bugfix: Model is wrong.
+* High: Time-sensitive project.
+* Normal.
+Please delete the ones that are not applicable
+-->
+* Critical Bugfix: Reason
+* High: Reason
+* Normal
 
-## Commit Queue Checklist:
-<!-- 
-Please complete all items in list. Make sure to attach logs from RT testing in comment, not in repository. Once all boxes are checked, please add the label "Ready for Commit Queue".
+## Git Tracking
+### UFSWM:
+<!--
+Please add the UFS-WM github issue here if there is one
+Please delete the one that is not applicable.
 -->
-- [ ] Link PR's from all sub-components involved in section below
-- [ ] Confirm reviews completed in ALL sub-component PR's
-- [ ] Add all appropriate labels to this PR.
-- [ ] Run full RT suite on either Hera/Cheyenne AND attach log to a PR comment.
-- [ ] Add list of any failed regression tests to "Anticipated changes to regression tests" section.
+* Closes #
+* None
 
-## Linked PR's and Issues:
+### Sub component Pull Requests:
 <!--
-Please link dependent pull requests.
-EXAMPLE: "- Depends on NOAA-EMC/fv3atm/pull/<pullrequest_number>"
+Please provide a list of sub-components involved with this pull request.
+Please provide links to the sub-component pull requests as shown below.
+Please delete what is not needed.
+Example:
+* FV3: NOAA-EMC/fv3atm#734
+  * ccpp-physics: ufs-community/ccpp-physics#33
+* WW3: NOAA-EMC/WW3#321
+-->
+* AQM:
+* CDEPS:
+* CICE:
+* CMEPS:
+* CMakeModules:
+* FV3:
+  * ccpp-physics:
+  * atmos_cubed_sphere:
+* GOCART:
+* HYCOM:
+* MOM6:
+* NOAHMP:
+* WW3:
+* stochastic_physics:
+* None
 
-Please link the related issues to be closed with this PR, whether in this repository, or in another repository.
-EXAMPLE: "- Closes NOAA-EMC/fv3atm/issues/<issue_number>"
+### UFSWM Blocking Dependencies:
+<!--
+If there are any UFSWM PR's that are needed to be completed before this one, please add links
+to them here
+Please delete what is not needed.
+-->
+* Blocked by #
+* None
 
-PLEASE MAKE SURE TO USE THE - with a space before the "Depends on" or "Closes" as they show up well on github.
+---
+## Changes
+### Regression Test Changes (Please commit test_changes.list):
+<!--
+Please let us know if this PR creates new baselines, changes baselines or not.
+Please delete what is not needed.
+Please make sure you have properly submitted test_changes.list
 -->
+* PR Adds New Tests/Baselines.
+* PR Updates/Changes Baselines.
+* No Baseline Changes.
 
-## Testing Day Checklist:
+### Input data Changes:
 <!--
-Please consult the ufs-weather-model [wiki](https://github.com/ufs-community/ufs-weather-model/wiki/Making-code-changes-in-the-UFS-weather-model-and-its-subcomponents) if you are unsure how to do this.
+If there are any changes to input-data for a test, please provide information here.
+Please delete what is not needed.
 -->
-- [ ] This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR.
-- [ ] Move new/updated input data on RDHPCS Hera and propagate input data changes to all supported systems.
+* None.
+* New input data.
+* Updated input data.
+
+### Library Changes/Upgrades:
+<!-- Library updates take time. Please provide library and version information here.
+** SPECIAL INSTRUCTIONS **
+If this PR needs updates to libraries please make sure to accomplish the following tasks:
+- Create separate issue in (https://github.com/JCSDA/spack-stack) asking for update to library. Include library name, library version.
+- Add issue link from JCSDA/spack-stack following this item <!-- for example: "* JCSDA/spack-stack#1757"
 
-### Testing Log (for CM's):
+Please delete what is not needed.
+-->
+* Required
+  * Library names w/versions:
+  * Git Stack Issue (JCSDA/spack-stack#)
+* No Updates
+
+---
+<!-- STOP!!! THE FOLLOWING IS FOR CODE MANAGERS ONLY. PLEASE DO NOT FILL OUT -->
+## Testing Log:
 - RDHPCS
   - [ ] Hera
   - [ ] Orion
+  - [ ] Hercules
   - [ ] Jet
   - [ ] Gaea
-  - [ ] Cheyenne
+  - [ ] Derecho
 - WCOSS2
   - [ ] Dogwood/Cactus
   - [ ] Acorn
-- CI
-  - [ ] Completed
-- opnReqTest
-  - [ ] N/A
-  - [ ] Log attached to comment
+- [ ] CI
+- [ ] opnReqTest (complete task if unnecessary)

.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

.gitignore

@@ -73,3 +73,8 @@ tests/fv3_conf/compile_qsub.IN
 tests/fv3_conf/fv3_slurm.IN
 tests/fv3_conf/fv3_qsub.IN
 build*.log*
+rocoto_workflow*
+fail_compile_*
+fail_test_*
+tests/run_dir
+tests/logs/log_*

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "FV3"]
   path = FV3
   url = https://github.com/HelinWei-NOAA/fv3atm
-  branch = nsoil9
+  branch = nsoilg
 [submodule "WW3"]
   path = WW3
   url = https://github.com/NOAA-EMC/WW3

.readthedocs.yaml

@@ -4,6 +4,10 @@
 
 # Required
 version: 2
+build: 
+  os: ubuntu-20.04
+  tools: 
+    python: "3.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -18,6 +22,5 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: doc/UsersGuide/requirements.txt

.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

CDEPS-interface/CMakeLists.txt

@@ -1,16 +1,20 @@
 # CDEPS compiler flags
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-  set(CMAKE_Fortran_FLAGS "-g -fbacktrace -ffree-line-length-none")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace -ffree-line-length-none")
+  #Set CPP defintions for the ufs/cdeps_share target library
+  list(APPEND CDEPS_SHARE_DEFS "CPRGNU")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch -fallow-invalid-boz")
   endif()
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -fcheck=bounds -ffpe-trap=invalid,zero,overflow,underflow" )
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
-  set(CMAKE_Fortran_FLAGS "-g -traceback")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -O -assume realloc_lhs")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -fp-model precise")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fpe0 -ftrapuv -init=snan,arrays")
+  #Set CPP defintions for the ufs/cdeps_share target library
+  list(APPEND CDEPS_SHARE_DEFS "CPRINTEL")
 else()
   message(WARNING "Fortran compiler with ID ${CMAKE_Fortran_COMPILER_ID} will be used with CMake default options")
 endif()
@@ -23,6 +27,7 @@ add_library(share OBJECT ${cdeps_share_files} ${ufs_cdeps_share_files})
 set_target_properties(share PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
 target_include_directories(share PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ufs/cdeps_share)
 target_include_directories(share PRIVATE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>)
+target_compile_definitions(share PRIVATE ${CDEPS_SHARE_DEFS})
 target_link_libraries(share PRIVATE esmf)
 
 # CDEPS/streams