Merge tag 'cam6_4_163' into cam_st-arch_dart

cam6_4_163: Refactor rad_constituents, aerosol_optics_cam for portability; extend abstract aerosol interface

Author: cacraigucar

.github/workflows/fleximod_test.yaml

@@ -13,7 +13,7 @@ jobs:
         uses: actions/checkout@v4
       - id: run-fleximod
         run: |
-          $GITHUB_WORKSPACE/bin/git-fleximod update
+          $GITHUB_WORKSPACE/bin/git-fleximod update -o
           echo
           echo "Update complete, checking status"
           echo
@@ -23,7 +23,7 @@ jobs:
           echo
           echo "Checking if git fleximod matches expected externals"
           echo
-          git diff --exit-code
+          git add . && git diff --exit-code && git diff --cached --exit-code
 #      - name: Setup tmate session
 #        if: ${{ failure() }}
 #        uses: mxschmitt/action-tmate@v3

.gitignore

@@ -2,6 +2,9 @@
 buildnmlc
 buildcppc
 
+# Ignore ide configs
+.vscode
+
 # Ignore editor temporaries and backups
 *~
 .#*

.gitmodules

@@ -2,23 +2,16 @@
 	path = chem_proc
 	url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
         fxrequired = AlwaysRequired
-        fxtag = chem_proc5_0_06
+        fxtag = chem_proc5_0_07
 	fxDONOTUSEurl = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
 
 [submodule "carma"]
 	path = src/physics/carma/base
 	url = https://github.com/ESCOMP/CARMA_base.git
         fxrequired = AlwaysRequired
-        fxtag = carma4_09
+        fxtag = carma4_10
         fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git
 
-[submodule "pumas"]
-        path = src/physics/pumas
-        url =  https://github.com/ESCOMP/PUMAS
-        fxrequired = AlwaysRequired
-        fxtag = pumas_cam-release_v1.38
-        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
-
 [submodule "pumas-frozen"]
 	path = src/physics/pumas-frozen
 	url = https://github.com/ESCOMP/PUMAS
@@ -30,15 +23,23 @@
 	path = src/physics/ali_arms
 	url = https://github.com/ESCOMP/ALI-ARMS
         fxrequired = AlwaysRequired
-        fxtag = ALI_ARMS_v1.0.1
+        fxtag = ALI_ARMS_v1.0.2
         fxDONOTUSEurl = https://github.com/ESCOMP/ALI-ARMS
 
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-        fxtag = atmos_phys0_13_000
+	fxtag = atmos_phys0_21_000
+        fxrequired = AlwaysRequired
+        fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
+
+[submodule "cam-sima"]
+        path = src/utils/cam-sima
+        url = https://github.com/ESCOMP/CAM-SIMA.git
         fxrequired = AlwaysRequired
-	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
+        fxsparse = ../.sima_phys_utils_sparse_checkout
+        fxtag = sima0_07_000
+        fxDONOTUSEurl = https://github.com/ESCOMP/CAM-SIMA.git
 
 [submodule "fv3"]
 	path = src/dynamics/fv3
@@ -51,14 +52,14 @@
 	path = src/chemistry/geoschem/geoschem_src
 	url = https://github.com/geoschem/geos-chem.git
         fxrequired = AlwaysRequired
-        fxtag = 14.4.3
+        fxtag = 14.5.3
         fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
 
 [submodule "cloud_j"]
 	path = src/chemistry/cloud_j
 	url = https://github.com/geoschem/cloud-j.git
         fxrequired = AlwaysRequired
-        fxtag = 7.7.3
+        fxtag = 8.0.1
         fxDONOTUSEurl = https://github.com/geoschem/cloud-j.git
 
 [submodule "hetp"]
@@ -71,17 +72,10 @@
 [submodule "hemco"]
 	path = src/hemco
 	url = https://github.com/ESCOMP/HEMCO_CESM.git
-        fxtag = hemco-cesm2_1_0_hemco3_9_0
+        fxtag = hemco-cesm2_2_0_hemco3_10_3
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
 
-[submodule "rte-rrtmgp"]
-	path = src/physics/rrtmgp/ext
-	url = https://github.com/earth-system-radiation/rte-rrtmgp.git
-        fxrequired = AlwaysRequired
-        fxtag = v1.7
-        fxDONOTUSEurl = https://github.com/earth-system-radiation/rte-rrtmgp.git
-
 [submodule "rrtmgp-data"]
 	path = src/physics/rrtmgp/data
 	url = https://github.com/earth-system-radiation/rrtmgp-data.git
@@ -102,7 +96,7 @@
 	url = https://github.com/CFMIP/COSPv2.0
         fxrequired = AlwaysRequired
         fxsparse = ../.cosp_sparse_checkout
-        fxtag = v2.1.4cesm
+        fxtag = v2.1.9
 	fxDONOTUSEurl = https://github.com/CFMIP/COSPv2.0
 
 [submodule "clubb"]
@@ -113,101 +107,108 @@
         fxtag = clubb_4ncar_20240605_73d60f6_gpufixes_posinf
         fxDONOTUSEurl = https://github.com/larson-group/clubb_release
 
-[submodule "cism"]
-path = components/cism
-url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_005
-fxrequired = ToplevelRequired
-fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+[submodule "ext_co2_cooling"]
+	path = src/physics/ext_co2_cooling
+	url = https://github.com/fedef17/CO2_cool_fort.git
+	fxrequired = AlwaysRequired
+	fxsparse = ../.ext_co2_cooling_sparse_checkout
+	fxtag = v1.1
+	fxDONOTUSEurl = https://github.com/fedef17/CO2_cool_fort.git
 
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_84
+fxtag = rtm1_0_89
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.07
+fxtag = mosart1.1.13
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n03_v2.2.0
+fxtag = v3.0.1
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.39
+fxtag = ccs_config_cesm1.0.79
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.72
+fxtag = cime6.1.169
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.39
+fxtag = cmeps1.1.41
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.69
+fxtag = cdeps1.0.93
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.9
+fxtag = share1.1.19
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_3
+fxtag = pio2_6_8
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
 [submodule "cice"]
 path = components/cice
 url = https://github.com/ESCOMP/CESM_CICE
-fxtag = cesm3_cice6_6_0_6
+fxtag = cesm3_cice6_6_3_5
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 
 [submodule "clm"]
 path = components/clm
 url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.3.017
+fxtag = ctsm5.4.024
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
 [submodule "fms"]
 path = libraries/FMS
 url = https://github.com/ESCOMP/FMS_interface
-fxtag = fi_240828
+fxtag = fi_250428
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
 
 [submodule "tools/CUPiD"]
 path = tools/CUPiD
 url = https://github.com/NCAR/CUPiD.git
-fxtag = v0.1.4
+fxtag = v0.5.1
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
 
+[submodule "tuv-x"]
+path = libraries/tuv-x
+url = https://github.com/NCAR/tuv-x.git
+fxtag = v0.14.3
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/tuv-x.git

.lib/git-fleximod/.github/workflows/pytest.yaml

@@ -18,7 +18,7 @@ jobs:
       # reference the matrixe python version here.
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.12'
 
       # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow
       # from installing Poetry every time, which can be slow. Note the use of the Poetry version
@@ -29,7 +29,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.local
-          key: poetry-1.7.1
+          key: poetry-1.8.2
 
       # Install Poetry. You could do this manually, or there are several actions that do this.
       # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to
@@ -42,7 +42,7 @@ jobs:
       # cache it.
       - uses: snok/install-poetry@v1
         with:
-          version: 1.7.1
+          version: 1.8.2
           virtualenvs-create: true
           virtualenvs-in-project: true
 
@@ -73,5 +73,7 @@ jobs:
       - run: |
           git config --global user.name "${GITHUB_ACTOR}"
           git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-          poetry run pytest
-
+          poetry run pytest --doctest-modules
+#      - name: Setup tmate session
+#        if: ${{ failure() }}
+#        uses: mxschmitt/action-tmate@v3

.lib/git-fleximod/.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: ^utils/.*$
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace

.lib/git-fleximod/CODE_OF_CONDUCT.md

@@ -17,7 +17,7 @@ Examples of behaviors that contribute to a positive environment include:
 * Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
 * Acknowledging the contributions of others
 * Avoid personal attacks directed toward other participants
-* Be mindful of your surroundings and of your fellow participants 
+* Be mindful of your surroundings and of your fellow participants
 * Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
 * Respect the rules and policies of the project and venue
 
@@ -29,7 +29,7 @@ Examples of unacceptable behavior include, but are not limited to:
 * Personal attacks directed at other guests, members, participants, etc.
 * Publishing others' private information, such as a physical or electronic address, without explicit permission
 * Alarming, intimidating, threatening, or hostile comments or conduct
-* Inappropriate use of nudity and/or sexual images 
+* Inappropriate use of nudity and/or sexual images
 * Threatening or stalking anyone, including a participant
 * Other conduct which could reasonably be considered inappropriate in a professional setting
 
@@ -60,7 +60,7 @@ the [Attribution](#attribution) section.
 ## Reporting
 Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as
 outlined in the [Consequences](#consequences) section below.
-However, making a report to a project administrator is not considered an 'official report' to UCAR. 
+However, making a report to a project administrator is not considered an 'official report' to UCAR.
 
 Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint
 Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's

.lib/git-fleximod/README.md

@@ -25,7 +25,7 @@ Git-fleximod is a Python-based tool that extends Git's submodule and sparse chec
 
 ## Supported .gitmodules Variables
 
-    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxtag: Specify a specific tag or hash to checkout for a submodule.  Branches are not acceptable.
     fxrequired: Mark a submodule's checkout behavior, with allowed values:
       - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module).
       - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module).