Remove manage_externals and update based on ESCOMP/CESM tag 'cesm3_0_beta01'

.gitignore

@@ -1,11 +1,3 @@
-# managed directories that are checked out by the externals tool
-cime/
-components/
-libraries/
-share/
-ccs_config/
-tools/statistical_ensemble_test/
-
 # generated local files
 *.log
 
@@ -15,3 +7,4 @@ tools/statistical_ensemble_test/
 
 # generated python files
 *.pyc
+__pycache__

.gitmodules

@@ -0,0 +1,197 @@
+# This is a git submodule file with additional support for
+# git-fleximod (https://github.com/jedwards4b/git-fleximod)
+#
+# The additional flags supported by git-fleximod are
+# fxtag - the tag associated with the submodule, this tag can be tested for
+#         consistancy with the submodule hash using git-fleximod status
+#         the hash can be updated to the tag using git-fleximod update
+#
+# fxrequired - indicates if a given submodule should be checked out on install
+#              submoudules can be toplevel or internal and required or optional
+#              toplevel means that the submodule should only be checked out if the
+#              module is the toplevel of the git repo (is not a submodule itself)
+#              internal means that the submodule is needed by the component whether
+#              the component is toplevel or the submodule of another repo
+#              required means that the submodule should always be checked out
+#              optional means that the submodule should only be checked out if the
+#              optional flag is provided to git-fleximod or the submodule name is
+#              explicitly listed on the git-fleximod command line.
+#
+# fxsparse -   this is a path to a git sparse checkout file indicating that the
+#              submodule should be checked out in sparse mode
+#
+# fxDONOTUSEurl    -   this field is used by git-fleximod test to insure that the url is pointing
+#              to the official url of the repo and not to an unofficial fork.
+#              It is intended for use of github workflows to test commits to protected
+#              repository branches.
+#
+
+
+[submodule "ccs_config"]
+	path = ccs_config
+	url = https://github.com/EarthWorksOrg/ccs_config_cesm.git
+	fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
+        fxtag = ccs_config-ew2.3.003
+        fxrequired = ToplevelRequired
+
+[submodule "share"]
+	path = share
+	url = https://github.com/ESCOMP/CESM_share
+	fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
+        fxtag = share1.0.19
+        fxrequired = ToplevelRequired
+
+[submodule "cime"]
+	path = cime
+	url = https://github.com/EarthWorksOrg/cime
+	fxDONOTUSEurl = https://github.com/ESMCI/cime
+        fxtag = cime-ew2.3.002
+        fxrequired = ToplevelRequired
+
+[submodule "mct"]
+	path = libraries/mct
+	url = https://github.com/MCSclimate/MCT
+	fxDONOTUSEurl = https://github.com/MCSclimate/MCT
+        fxrequired = ToplevelRequired
+        fxtag = MCT_2.11.0
+
+[submodule "mpi-serial"]
+	path = libraries/mpi-serial
+	url = https://github.com/ESMCI/mpi-serial
+	fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial
+        fxtag = MPIserial_2.5.0
+        fxrequired = ToplevelRequired
+
+[submodule "cam"]
+	path = components/cam
+	url = https://www.github.com/EarthWorksOrg/CAM
+	fxDONOTUSEurl = https://www.github.com/ESCOMP/CAM
+        fxtag = cam-ew2.3.002
+        fxrequired = ToplevelRequired
+
+# EarthWorks is not using ww3
+# [submodule "ww3"]
+# 	path = components/ww3
+# 	url = https://github.com/ESCOMP/WW3_interface
+# 	fxDONOTUSEurl = https://github.com/ESCOMP/WW3_interface
+#         fxtag = ww3i_0.0.2
+#         fxrequired = ToplevelRequired
+
+# EarthWorks is not using rtm
+# [submodule "rtm"]
+# 	path = components/rtm
+# 	url = https://github.com/ESCOMP/RTM
+# 	fxDONOTUSEurl = https://github.com/ESCOMP/RTM
+#         fxrequired = ToplevelRequired
+#         fxtag = rtm1_0_79 
+
+[submodule "pysect"]
+	path = tools/statistical_ensemble_test/pyCECT
+	url = https://github.com/NCAR/PyCECT
+	fxDONOTUSEurl = https://github.com/NCAR/PyCECT
+        fxrequired = ToplevelRequired
+        fxtag = 3.2.2
+
+[submodule "mosart"]
+	path = components/mosart
+	url = https://github.com/ESCOMP/MOSART
+	fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
+        fxrequired = ToplevelRequired
+        fxtag = mosart1_0_49
+
+# EarthWorks is not using mizuroute
+# [submodule "mizuroute"]
+# 	path = components/mizuroute
+# 	url = https://github.com/ESCOMP/mizuRoute
+# 	fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
+#         fxrequired = ToplevelRequired
+#         fxtag = cesm-coupling.n02_v2.1.2
+
+# EarthWorks is not using fms
+# [submodule "fms"]
+# 	path = libraries/FMS
+# 	url = https://github.com/ESCOMP/FMS_interface
+# 	fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface
+#         fxrequired = ToplevelRequired
+#         fxtag = fi_240516
+
+[submodule "parallelio"]
+	path = libraries/parallelio
+	url = https://github.com/NCAR/ParallelIO
+	fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
+        fxrequired = ToplevelRequired
+        fxtag = pio2_6_2
+
+[submodule "cdeps"]
+	path = components/cdeps
+	url = https://github.com/ESCOMP/CDEPS
+	fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS
+        fxrequired = ToplevelRequired
+        fxtag = cdeps1.0.37
+
+[submodule "cmeps"]
+	path = components/cmeps
+	url = https://github.com/EarthWorksOrg/CMEPS.git
+	fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
+        fxrequired = ToplevelRequired
+        fxtag = cmeps-ew2.3.002
+
+[submodule "cice"]
+	path = components/cice
+	url = https://github.com/ESCOMP/CESM_CICE
+	fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
+        fxrequired = ToplevelRequired
+        fxtag = cesm_cice6_5_0_9
+
+# EarthWorks is not using cism
+# [submodule "cism"]
+# 	path = components/cism
+# 	url = https://github.com/ESCOMP/cism-wrapper.git
+# 	fxDONOTUSEurl = https://github.com/ESCOMP/cism-wrapper.git
+#         fxtag = cismwrap_2_2_001
+#         fxrequired = ToplevelRequired
+
+[submodule "clm"]
+	path = components/clm
+	url = https://github.com/EarthWorksOrg/CTSM
+	fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
+        fxrequired = ToplevelRequired
+        fxtag = ctsm-ew2.3.002
+
+# EarthWorks is not using mom
+# [submodule "mom"]
+# 	path = components/mom
+# 	url = https://github.com/ESCOMP/MOM_interface
+# 	fxDONOTUSEurl = https://github.com/ESCOMP/MOM_interface
+#         fxrequired = ToplevelRequired
+#         fxtag = mi_240522
+
+# EarthWorks-specific
+[submodule "mpas-ocean"]
+	path = components/mpas-ocean
+	url = https://github.com/EarthWorksOrg/mpas-ocean.git
+	fxDONOTUSEurl = https://github.com/EarthWorksOrg/mpas-ocean.git
+			fxrequired = ToplevelRequired
+			fxtag = mpaso-ew2.3.000
+
+[submodule "mpas-seaice"]
+	path = components/mpas-seaice
+	url = https://github.com/EarthWorksOrg/mpas-seaice.git
+	fxDONOTUSEurl = https://github.com/EarthWorksOrg/mpas-seaice.git
+			fxrequired = ToplevelRequired
+			fxtag = mpassi-ew2.3.000
+
+[submodule "mpas-framework"]
+	path = components/mpas-framework
+	url = https://github.com/EarthWorksOrg/mpas-framework.git
+	fxDONOTUSEurl = https://github.com/EarthWorksOrg/mpas-framework.git
+			fxrequired = ToplevelRequired
+			fxtag = mpasfrwk-ew2.3.000
+
+[submodule "ewms-diags"]
+	path = tools/ewms-diags
+	url = https://github.com/EarthWorksOrg/EarthWorks_diags
+	fxDONOTUSEurl = https://github.com/EarthWorksOrg/EarthWorks_diags
+			fxrequired = ToplevelRequired
+			fxtag = diags-ew1.0.000
+

.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/[email protected]

.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