Update to develop and add pre-test RT logs PR #1

.github/linters/.yaml-lint.yml

@@ -0,0 +1,28 @@
+---
+
+extends: default
+
+rules:
+  braces:
+    level: warning
+    max-spaces-inside: 1
+  brackets:
+    level: warning
+    max-spaces-inside: 1
+  colons:
+    level: warning
+  commas: disable
+  comments: disable
+  comments-indentation: disable
+  document-start: disable
+  empty-lines:
+    level: warning
+  hyphens:
+    level: warning
+  indentation:
+    level: warning
+    indent-sequences: consistent
+  line-length: disable
+  truthy: disable
+  trailing-spaces: disable
+

.github/workflows/aux.yml

@@ -18,43 +18,42 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - name: Share helper id
-      run: echo -n ${{ github.run_id }} >~/id_file
+      - name: Share helper id
+        run: echo -n ${{ github.run_id }} >~/id_file
 
-    - uses: actions/cache@v2
-      with:
-        path: ~/id_file
-        key: helperid-${{ github.event.workflow_run.id }}
+      - uses: actions/cache@v4
+        with:
+          path: ~/id_file
+          key: helperid-${{ github.event.workflow_run.id }}
 
   repocheck:
     name: Repo check
     runs-on: ubuntu-20.04
 
     steps:
-    - name: Check up-to-dateness and post comment
-      run: |
-        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.pull_request.head.repo.owner.login }}
-        echo "pr_uid is $pr_uid"
-        ./repo_check.sh
-        #comment="$(./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": "'"${comment}"'"}'
-        #  echo -n "failure" >~/repocheck_file
-        #else
-        #  echo -n "success" >~/repocheck_file
-        #fi
-        
+      - name: Check up-to-dateness and post comment
+        run: |
+          trap 'echo "exit-code=$?" >> "$GITHUB_OUTPUT"' EXIT
+          head_sha=${{ 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.pull_request.head.repo.owner.login }}
+          echo "pr_uid is $pr_uid"
+          ./repo_check.sh
+          #comment="$(./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/build_test.yml

@@ -16,12 +16,12 @@ jobs:
       current: ${{ steps.check.outputs.current }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Wait for caching source
       run: sleep 30
 
-    - uses: actions/cache@v2
+    - uses: actions/cache@v4
       with:
         path: ~/id_file
         key: helperid-${{ github.run_id }}

.github/workflows/superlinter.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Super-Linter
         uses: super-linter/[email protected]
         env:
-          LINTER_RULES_PATH: /
+          LINTER_RULES_PATH: '.github/linters/'
           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).*
@@ -33,5 +33,5 @@ jobs:
           #VALIDATE_GITHUB_ACTIONS: true
           #VALIDATE_LUA: true
           #VALIDATE_MARKDOWN: true
-          #VALIDATE_PYTHON_PYLINT: true
-          #VALIDATE_YAML: 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_*

MOM6-interface/mom6_files.cmake

@@ -36,6 +36,7 @@ list(APPEND mom6_src_files
   MOM6/src/core/MOM_continuity_PPM.F90
   MOM6/src/core/MOM_density_integrals.F90
   MOM6/src/core/MOM_dynamics_split_RK2.F90
+  MOM6/src/core/MOM_dynamics_split_RK2b.F90
   MOM6/src/core/MOM_dynamics_unsplit.F90
   MOM6/src/core/MOM_dynamics_unsplit_RK2.F90
   MOM6/src/core/MOM_forcing_type.F90
@@ -59,6 +60,7 @@ list(APPEND mom6_src_files
   MOM6/src/diagnostics/MOM_sum_output.F90
   MOM6/src/diagnostics/MOM_wave_speed.F90
 
+  MOM6/src/equation_of_state/MOM_EOS_base_type.F90
   MOM6/src/equation_of_state/MOM_EOS.F90
   MOM6/src/equation_of_state/MOM_EOS_Jackett06.F90
   MOM6/src/equation_of_state/MOM_EOS_Roquet_SpV.F90

cmake/Intel.cmake

@@ -20,7 +20,8 @@ endif()
 
 if(DEBUG)
     add_definitions(-DDEBUG)
-    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
+    #set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
+    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
     set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -ftrapuv")
 else()
     if(FASTER)

doc/UsersGuide/requirements.txt

@@ -8,7 +8,7 @@ alabaster==0.7.16
     # via sphinx
 babel==2.14.0
     # via sphinx
-certifi==2024.2.2
+certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
     # via requests

doc/UsersGuide/source/Glossary.rst

@@ -68,7 +68,8 @@ Glossary
       Global atmospheric model based on fluid dynamics principles, including Euler's equations of motion.
 
    EMC
-      The `Environmental Modeling Center <https://www.emc.ncep.noaa.gov/emc.php>`_ is one of :term:`NCEP`'s nine centers and leads the :term:`National Weather Service <NWS>`'s modeling efforts.
+      The `Environmental Modeling Center <https://www.emc.ncep.noaa.gov/emc.php>`__ is one of :term:`NCEP`'s nine centers and leads the :term:`National Weather Service <NWS>`'s modeling efforts.
+
 
    ESMF
       `Earth System Modeling Framework <https://earthsystemmodeling.org/docs/release/latest/ESMF_usrdoc/>`__. The ESMF defines itself as "a suite of software tools for developing high-performance, multi-component Earth science modeling applications." It is a community-developed software infrastructure for building and coupling models. 

doc/UsersGuide/source/InputsOutputs.rst

@@ -1304,6 +1304,26 @@ These field section entries are described in :numref:`Table %s <FieldDescription
 
 Comments can be added to the diag_table using the hash symbol (``#``).
 
+
+Each WM component has its own ``diag_table`` with associated variables. :numref:`Table %s <diag-table-options>` contains links to the full set of options for each WM component.
+
+.. _diag-table-options:
+
+.. list-table:: * *diag_table* Options for WM Components*
+   :widths: 16 24 24
+   :header-rows: 1
+
+   * - WM Component
+     - Diag Table
+     - Source File
+   * - FV3
+     - :ref:`FV3 Variables <fv3diagtable>`
+     - `GFS_diagnostics.F90 <https://github.com/NOAA-EMC/fv3atm/blob/develop/ccpp/driver/GFS_diagnostics.F90>`_
+   * - MOM6
+     - `MOM6 Variables <https://ncar.github.io/MOM6/APIs/namespacemom__diagnostics.html>`_
+     - `MOM_diagnostics.F90 <https://github.com/NOAA-EMC/MOM6/blob/main/src/diagnostics/MOM_diagnostics.F90>`_
+
+
 A brief example of the diag_table is shown below.  ``"..."`` denotes where lines have been removed.
 
 .. _code-block-fv3-diag-table:

doc/UsersGuide/source/conf.py

@@ -92,6 +92,7 @@
                             ]
 # Ignore working links that cause a linkcheck 403 error.
 linkcheck_ignore = [r'https://agupubs\.onlinelibrary\.wiley\.com/doi/10\.1029/2020MS002260',
+                    r'https://glossary.ametsoc.org/wiki/*',
                    ]
 
 # -- Options for HTML output -------------------------------------------------

doc/UsersGuide/source/tables/fv3_diag_table.rst

@@ -0,0 +1,13 @@
+:orphan:
+
+.. _fv3diagtable:
+
+****************************
+FV3 Weather Model Variables
+****************************
+
+
+.. csv-table::
+    :file: fv3diagtable.csv
+    :widths: 10, 15
+    :header-rows: 1