Merge remote-tracking branch 'remotes/origin/feature/hafs.v2.0.1' int…

…o feature/mn_noahmp

.github/pull_request_template.md

@@ -1,91 +1,153 @@
-<!-- THE FOLLOWING IS FOR THE PR AUTHOR TO FILL OUT
-PLEASE DO NOT MODIFY THE TEMPLATE BEYOND FILLING OUT THE PROPER SECTIONS -->
-## PR Author Checklist:
-<!--  Please complete all items in list. -->
-- [ ] I have linked PR's from all sub-components involved in section below. <!-- PLEASE DO NOT LINK SUBCOMPONENT ISSUES -->
-- [ ] I am confirming reviews are completed in ALL sub-component PR's.
-- [ ] I have run the full RT suite on either Hera/Cheyenne AND have attached the log to this PR below this line:
-  - LOG: 
-- [ ] I have added the list of all failed regression tests to "Anticipated changes" section.
-- [ ] I have filled out all sections of the template.
-
-## Description
-<!-- Provide a detailed description of what this PR does in the space provided below-->
-
-
-## Linked Issues and Pull Requests
-### Associated UFSWM Issue to close
-<!-- Example: "- Closes #1698" -->
-
-
-### Subcomponent Pull Requests
-<!-- format: - <community>/<repo>/pull/<PR number> i.e.: - NOAA-EMC/fv3atm/pull/33 or "None" -->
-
-
-### Blocking Dependencies
-<!-- Example: "- Depends on #1733" or "None" -->
-
-
-### Subcomponents involved:
-- [ ] AQM
-- [ ] CDEPS
-- [ ] CICE
-- [ ] CMEPS
-- [ ] CMakeModules
-- [ ] FV3
-- [ ] GOCART
-- [ ] HYCOM
-- [ ] MOM6
-- [ ] NOAHMP
-- [ ] WW3
-- [ ] stochastic_physics
-- [ ] none
-
-## Anticipated Changes
-### Input data
-- [ ] No changes are expected to input data.
-- [ ] Changes are expected to input data:
-  - [ ] New input data.
-  - [ ] Updated input data.
-
-### 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 in the space provided below -->
-<details><summary>Tests effected by changes in this PR:</summary>
-<!-- ADD ITEMS HERE or add "None" -->
-
-</details>
-
-### Libraries
-<!-- Library updates take time. If this PR needs updates to libraries, please make sure to accomplish the following tasks -->
-- [ ] Not Needed
-- [ ] 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" -->
-
-
-<!-- THE FOLLOWING IS FOR CODE MANAGERS ONLY DO NOT FILL OUT -->
-<details><summary>Code Managers Log</summary>
-
-- [ ] 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.
-  - [ ] N/A
-
-### Testing Log:
+<!-- 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:
+<!--
+Please provide a detailed verbose description of what this PR does
+-->
+
+
+### 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 - 
+```
+
+### 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
+
+## Git Tracking
+### UFSWM:
+<!--
+Please add the UFS-WM github issue here if there is one
+Please delete the one that is not applicable.
+-->
+* Closes #
+* None
+
+### Sub component Pull Requests:
+<!--
+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
+
+### 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
+
+---
+## 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.
+
+### Input data Changes:
+<!--
+If there are any changes to input-data for a test, please provide information here.
+Please delete what is not needed.
+-->
+* 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"
+
+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
-</details>
+- [ ] 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

.gitmodules

@@ -1,11 +1,11 @@
 [submodule "FV3"]
   path = FV3
   url = https://github.com/hafs-community/fv3atm
-  branch = feature/hafsv2_baseline
+  branch = feature/mn_moahmp
 [submodule "WW3"]
   path = WW3
   url = https://github.com/hafs-community/WW3
-  branch = feature/hafsv2_baseline
+  branch = feature/hafs.v2.0.1
 [submodule "stochastic_physics"]
   path = stochastic_physics
   url = https://github.com/NOAA-PSL/stochastic_physics
@@ -16,10 +16,8 @@
   branch = develop
 [submodule "CMEPS"]
   path = CMEPS-interface/CMEPS
-  #url = https://github.com/NOAA-EMC/CMEPS
-  #branch = emc/develop
-  url = https://github.com/hafs-community/CMEPS
-  branch = feature/hafsv2_baseline
+  url = https://github.com/NOAA-EMC/CMEPS
+  branch = emc/develop
 [submodule "HYCOM"]
   path = HYCOM-interface/HYCOM
   url = https://github.com/NOAA-EMC/HYCOM-src
@@ -34,10 +32,8 @@
   branch = emc/develop
 [submodule "CDEPS"]
   path = CDEPS-interface/CDEPS
-  #url = https://github.com/NOAA-EMC/CDEPS
-  #branch = develop
-  url = https://github.com/hafs-community/CDEPS
-  branch = feature/hafsv2_baseline
+  url = https://github.com/NOAA-EMC/CDEPS
+  branch = develop
 [submodule "GOCART"]
   path = GOCART
   url = https://github.com/GEOS-ESM/GOCART

.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