Merge tag 'cam-ew2.3.004' into add_v8mpasfiles_eworg2

Bring in dev changes from EarthWorksOrg/CAM

.gitignore

@@ -1,27 +1,3 @@
-# Ignore externals
-ccs_config
-chem_proc
-cime
-components
-manage_externals.log
-src/physics/ali_arms/
-src/physics/carma/base
-src/physics/clubb
-src/physics/cosp2/src
-src/physics/silhs
-src/chemistry/geoschem/geoschem_src
-src/physics/pumas
-src/physics/pumas-frozen
-src/physics/rrtmgp/data
-src/physics/rrtmgp/ext
-src/dynamics/fv3/atmos_cubed_sphere
-libraries/FMS
-libraries/mct
-libraries/parallelio
-src/atmos_phys
-src/dynamics/mpas/dycore
-share
-src/hemco
 # Ignore compiled python
 buildnmlc
 buildcppc

.gitmodules

@@ -0,0 +1,192 @@
+[submodule "chem_proc"]
+	path = chem_proc
+	url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
+        fxrequired = AlwaysRequired
+        fxtag = chem_proc5_0_06
+	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_01
+        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_v1.36
+        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
+
+[submodule "pumas-frozen"]
+	path = src/physics/pumas-frozen
+	url = https://github.com/ESCOMP/PUMAS
+        fxrequired = AlwaysRequired
+        fxtag = pumas_cam-release_v1.17_rename
+        fxDONOTUSEurl = https://github.com/ESCOMP/PUMAS
+
+[submodule "ali_arms"]
+	path = src/physics/ali_arms
+	url = https://github.com/ESCOMP/ALI-ARMS
+        fxrequired = AlwaysRequired
+        fxtag = ALI_ARMS_v1.0.1
+        fxDONOTUSEurl = https://github.com/ESCOMP/ALI-ARMS
+
+[submodule "atmos_phys"]
+	path = src/atmos_phys
+	url = https://github.com/ESCOMP/atmospheric_physics
+        fxtag = atmos_phys0_03_000
+        fxrequired = AlwaysRequired
+	fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
+
+[submodule "fv3"]
+	path = src/dynamics/fv3
+	url = https://github.com/ESCOMP/CAM_FV3_interface.git
+        fxrequired = AlwaysRequired
+        fxtag = fv3int_061924
+	fxDONOTUSEurl = https://github.com/ESCOMP/CAM_FV3_interface.git
+
+[submodule "geoschem"]
+	path = src/chemistry/geoschem/geoschem_src
+	url = https://github.com/geoschem/geos-chem.git
+        fxrequired = AlwaysRequired
+        fxtag = 14.1.2
+        fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
+
+[submodule "hemco"]
+	path = src/hemco
+	url = https://github.com/ESCOMP/HEMCO_CESM.git
+        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm_rme01
+        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
+        fxrequired = AlwaysRequired
+        fxtag = v1.8
+        fxDONOTUSEurl = https://github.com/earth-system-radiation/rrtmgp-data.git
+
+[submodule "mpas"]
+	path = src/dynamics/mpas/dycore
+	url = https://github.com/EarthWorksOrg/MPAS-Model.git
+        fxrequired = AlwaysRequired
+        fxsparse = ../.mpas_sparse_checkout
+        fxtag = mpas-ew2.3.001
+	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
+
+[submodule "cosp2"]
+	path = src/physics/cosp2/src
+	url = https://github.com/CFMIP/COSPv2.0
+        fxrequired = AlwaysRequired
+        fxsparse = ../.cosp_sparse_checkout
+        fxtag = v2.1.4cesm
+	fxDONOTUSEurl = https://github.com/CFMIP/COSPv2.0
+
+[submodule "clubb"]
+	path = src/physics/clubb
+	url = https://github.com/larson-group/clubb_release
+        fxrequired = AlwaysRequired
+        fxsparse = ../.clubb_sparse_checkout
+        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_002
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
+
+[submodule "rtm"]
+path = components/rtm
+url = https://github.com/ESCOMP/RTM
+fxtag = rtm1_0_80
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/RTM
+
+[submodule "mosart"]
+path = components/mosart
+url = https://github.com/ESCOMP/MOSART
+fxtag = mosart1.1.02
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
+
+[submodule "mizuRoute"]
+path = components/mizuRoute
+url = https://github.com/ESCOMP/mizuRoute
+fxtag = cesm-coupling.n02_v2.1.3
+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_cesm1.0.0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
+
+[submodule "cime"]
+path = cime
+url = https://github.com/ESMCI/cime
+fxtag = cime6.1.0
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESMCI/cime
+
+[submodule "cmeps"]
+path = components/cmeps
+url = https://github.com/ESCOMP/CMEPS.git
+fxtag = cmeps1.0.2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
+
+[submodule "cdeps"]
+path = components/cdeps
+url = https://github.com/ESCOMP/CDEPS.git
+fxtag = cdeps1.0.45
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+
+[submodule "share"]
+path = share
+url = https://github.com/ESCOMP/CESM_share
+fxtag = share1.1.2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
+
+[submodule "parallelio"]
+path = libraries/parallelio
+url = https://github.com/NCAR/ParallelIO
+fxtag = pio2_6_2
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+
+[submodule "cice"]
+path = components/cice
+url = https://github.com/ESCOMP/CESM_CICE
+fxtag = cesm_cice6_5_0_10
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
+
+[submodule "clm"]
+path = components/clm
+url = https://github.com/ESCOMP/CTSM
+fxtag = ctsm5.2.009
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
+
+[submodule "fms"]
+path = libraries/FMS
+url = https://github.com/ESCOMP/FMS_interface
+fxtag = fi_240516
+fxrequired = ToplevelRequired
+fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
+

.lib/git-fleximod/.github/workflows/pre-commit

@@ -0,0 +1,13 @@
+name: pre-commit
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0

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

@@ -0,0 +1,77 @@
+# Run this job on pushes to `main`, and for pull requests. If you don't specify
+# `branches: [main], then this actions runs _twice_ on pull requests, which is
+# annoying.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and
+      # reference the matrixe python version here.
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      # 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
+      # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache
+      # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be
+      # mildly cleaner by using an environment variable, but I don't really care.
+      - name: cache poetry install
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: poetry-1.7.1
+
+      # 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
+      # Poetry's default install script, which feels correct. I pin the Poetry version here
+      # because Poetry does occasionally change APIs between versions and I don't want my
+      # actions to break if it does.
+      #
+      # The key configuration value here is `virtualenvs-in-project: true`: this creates the
+      # venv as a `.venv` in your testing directory, which allows the next step to easily
+      # cache it.
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.7.1
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache
+      # key: if you're using multiple Python versions, or multiple OSes, you'd need to include
+      # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock.
+      - name: cache deps
+        id: cache-deps
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+
+      # Install dependencies. `--no-root` means "install all dependencies but not the project
+      # itself", which is what you want to avoid caching _your_ code. The `if` statement
+      # ensures this only runs on a cache miss.
+      - run: poetry install --no-interaction --no-root
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+
+      # Now install _your_ project. This isn't necessary for many types of projects -- particularly
+      # things like Django apps don't need this. But it's a good idea since it fully-exercises the
+      # pyproject.toml and makes that if you add things like console-scripts at some point that
+      # they'll be installed and working.
+      - run: poetry install --no-interaction
+
+      # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml`
+      # so this line is super-simple. But it could be as complex as you need.
+      - run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+          poetry run pytest
+

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

@@ -0,0 +1,18 @@
+exclude: ^utils/.*$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.11.1
+    hooks:
+      - id: pylint
+        args:
+          - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member