Remove manage externals

.github/workflows/fleximod-test.yml

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+on:
+  push:
+    branches:
+      - master
+      - remove_manage_externals
+  pull_request:
+    branches:
+      - master
+      - remove_manage_externals
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.11"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: git-fleximod test
+      run: |
+        $GITHUB_WORKSPACE/bin/git-fleximod test

.gitmodules

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+# 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
+#
+# fxurl    -   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/ESMCI/ccs_config_cesm.git
+	fxurl = https://github.com/ESMCI/ccs_config_cesm.git
+        fxtag = ccs_config_cesm0.0.88
+        fxrequired = T:T
+
+[submodule "share"]
+	path = share
+	url = https://github.com/ESCOMP/CESM_share
+	fxurl = https://github.com/ESCOMP/CESM_share
+        fxtag = share1.0.18
+        fxrequired = T:T
+
+[submodule "cime"]
+	path = cime
+	url = https://github.com/jedwards4b/cime
+	fxurl = https://github.com/ESMCI/cime
+        fxtag = cime6.0.198_rme05
+        fxrequired = T:T
+
+[submodule "mct"]
+        path = libraries/mct
+	url = https://github.com/MCSclimate/MCT
+	fxurl = https://github.com/MCSclimate/MCT
+        fxrequired = T:T
+        fxtag = MCT_2.11.0
+
+[submodule "mpi-serial"]
+	path = libraries/mpi-serial
+	url = https://github.com/ESMCI/mpi-serial
+	fxurl = https://github.com/ESMCI/mpi-serial
+        fxtag = MPIserial_2.5.0
+        fxrequired = T:T
+
+[submodule "cpl7"]
+	path = components/cpl7
+	url = https://github.com/ESCOMP/CESM_CPL7andDataComps
+	fxurl = https://github.com/ESCOMP/CESM_CPL7andDataComps
+        fxtag = cpl77.0.7
+        fxrequired = T:T
+
+[submodule "cam"]
+	path = components/cam
+	url = https://www.github.com/jedwards4b/CAM
+	fxurl = https://www.github.com/ESCOMP/CAM
+        fxtag = cam6_3_143_rme01
+        fxrequired = T:T
+
+[submodule "ww3"]
+	path = components/ww3
+	url = https://github.com/ESCOMP/WW3-CESM
+	fxurl = https://github.com/ESCOMP/WW3-CESM
+        fxtag = ww3_221108
+        fxrequired = T:T
+
+[submodule "ww3dev"]
+	path = components/ww3dev
+       	url = https://github.com/jedwards4b/WW3_interface       
+       	fxurl = https://github.com/ESCOMP/WW3_interface       
+        fxtag = main_0.0.13_rme02
+        fxrequired = T:T
+
+[submodule "rtm"]
+	path = components/rtm
+	url = https://github.com/ESCOMP/RTM
+	fxurl = https://github.com/ESCOMP/RTM
+        fxrequired = T:T
+        fxtag = rtm1_0_78 
+
+[submodule "pysect"]
+	path = tools/statistical_ensemble_test/pyCECT
+	url = https://github.com/NCAR/PyCECT
+	fxurl = https://github.com/NCAR/PyCECT
+        fxrequired = T:T
+        fxtag = 3.2.2
+
+[submodule "mosart"]
+	path = components/mosart
+	url = https://github.com/ESCOMP/MOSART
+	fxurl = https://github.com/ESCOMP/MOSART
+        fxrequired = T:T
+        fxtag = mosart1_0_48
+
+[submodule "mizuroute"]
+	path = components/mizuroute
+	url = https://github.com/jedwards4b/mizuRoute
+	fxurl = https://github.com/ESCOMP/mizuRoute
+        fxrequired = T:T
+        fxtag = cesm-coupling.n02_v2.1.2_rme02
+
+[submodule "fms"]
+	path = libraries/FMS
+	url = https://github.com/jedwards4b/FMS_interface
+	fxurl = https://github.com/ESCOMP/FMS_interface
+        fxrequired = T:T
+        fxtag = fi_230818_rme01
+
+[submodule "parallelio"]
+	path = libraries/parallelio
+	url = https://github.com/NCAR/ParallelIO
+	fxurl = https://github.com/NCAR/ParallelIO
+        fxrequired = T:T
+        fxtag = pio2_6_2
+
+[submodule "cdeps"]
+	path = components/cdeps
+	url = https://github.com/jedwards4b/CDEPS
+	fxurl = https://github.com/ESCOMP/CDEPS
+        fxrequired = T:T
+        fxtag = cdeps1.0.26_rme01
+
+[submodule "cmeps"]
+	path = components/cmeps
+	url = https://github.com/ESCOMP/CMEPS.git
+	fxurl = https://github.com/ESCOMP/CMEPS.git
+        fxrequired = T:T
+        fxtag = cmeps0.14.49
+
+[submodule "cice5"]
+	path = components/cice5
+	url = https://github.com/ESCOMP/CESM_CICE5
+	fxurl = https://github.com/ESCOMP/CESM_CICE5
+        fxrequired = T:T
+        fxtag = cice5_20220204
+
+[submodule "cice6"]
+	path = components/cice
+	url = https://github.com/jedwards4b/CESM_CICE
+	fxurl = https://github.com/ESCOMP/CESM_CICE
+        fxrequired = T:T
+        fxtag = cesm_cice6_4_1_10_rme01
+
+[submodule "cism"]
+	path = components/cism
+	url = https://github.com/jedwards4b/cism-wrapper.git
+	fxurl = https://github.com/ESCOMP/cism-wrapper.git
+        fxtag = cismwrap_2_1_96_rme02
+        fxrequired = T:T
+
+[submodule "clm"]
+	path = components/clm
+	url = https://github.com/jedwards4b/CTSM
+	fxurl = https://github.com/ESCOMP/CTSM
+        fxrequired = T:T
+        fxtag = branch_tags/CESM3_dev.n04_ctsm5.1.dev145_rme02
+
+[submodule "mom"]
+	path = components/mom
+	url = https://github.com/jedwards4b/MOM_interface
+	fxurl = https://github.com/ESCOMP/MOM_interface
+        fxrequired = T:T
+        fxtag = mi_231107_rme01
+
+[submodule "pop"]
+	path = components/pop
+	url = https://github.com/jedwards4b/POP2-CESM
+	fxurl = https://github.com/ESCOMP/POP2-CESM
+        fxrequired = T:T
+        fxtag = cesm_pop_2_1_20231208_rme02

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

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+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/.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

.lib/git-fleximod/License

@@ -0,0 +1,20 @@
+Copyright 2024 National Center for Atmospheric Sciences (NCAR)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+“Software”), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

.lib/git-fleximod/README.md

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+# git-fleximod
+
+Flexible Submodule Management for Git
+
+## Overview
+
+Git-fleximod is a Python-based tool that extends Git's submodule capabilities, offering additional features for managing submodules in a more flexible and efficient way.
+
+## Installation
+
+#TODO    Install using pip:
+#        pip install git-fleximod
+  If you choose to locate git-fleximod in your path you can access it via command: git fleximod
+
+## Usage
+
+    Basic Usage:
+        git fleximod <command> [options]
+    Available Commands:
+        checkout: Checkout submodules according to git submodule hash configuration.
+        status: Display the status of submodules.
+        update: Update submodules to the tag indicated in .gitmodules variable fxtag.
+        test: Make sure that fxtags and submodule hashes are consistant,
+              make sure that official urls (as defined by fxurl) are set
+              make sure that fxtags are defined for all submodules
+    Additional Options:
+        See git fleximod --help for more details.
+
+## Supported .gitmodules Variables
+
+    fxtag: Specify a specific tag or branch to checkout for a submodule.
+    fxrequired: Mark a submodule's checkout behavior, with allowed values:
+      - T:T: Top-level and required (checked out only when this is the Toplevel module).
+      - T:F: Top-level and optional (checked out with --optional flag if this is the Toplevel module).
+      - I:T: Internal and required (always checked out).
+      - I:F: Internal and optional (checked out with --optional flag).
+    fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths.
+    fxurl: This is the url used in the test subcommand to assure that protected branches do not point to forks
+
+## Sparse Checkouts
+
+    To enable sparse checkout for a submodule, set the fxsparse variable
+    in the .gitmodules file to the path of a file containing the desired
+    sparse checkout paths. Git-fleximod will automatically configure
+    sparse checkout based on this file when applicable commands are run.
+    See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set)
+    for details on the format of this file.
+
+## Tests
+
+   The git fleximod test action is designed to be used by, for example, github workflows
+   to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags
+
+## Examples
+
+Here are some common usage examples:
+
+Checkout submodules, including optional ones:
+```bash
+  git fleximod checkout --optional
+```
+
+Updating a specific submodule to the fxtag indicated in .gitmodules:
+
+```bash
+    git fleximod update submodule-name
+```
+Example .gitmodules entry:
+```ini, toml
+    [submodule "cosp2"]
+        path = src/physics/cosp2/src
+        url = https://github.com/CFMIP/COSPv2.0
+        fxsparse = ../.cosp_sparse_checkout
+        fxtag = v2.1.4cesm
+```
+Explanation:
+
+This entry indicates that the submodule named cosp2 at tag v2.1.4cesm
+should be checked out into the directory src/physics/cosp2/src
+relative to the .gitmodules directory.  It should be checked out from
+the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as
+described in the file ../.cosp_sparse_checkout relative to the path
+directory.
+
+Additional example:
+```ini, toml
+    [submodule "cime"]
+        path = cime
+        url = https://github.com/jedwards4b/cime
+        fxrequired = T:T
+        fxtag = cime6.0.198_rme01
+```
+
+Explanation:
+
+This entry indicates that the submodule cime should be checked out
+into a directory named cime at tag cime6.0.198_rme01 from the URL
+https://github.com/jedwards4b/cime.  This should only be done if
+the .gitmodules file is at the top level of the repository clone.
+
+## Contributing
+
+We welcome contributions! Please see the CONTRIBUTING.md file for guidelines.
+
+## License
+
+Git-fleximod is released under the MIT License.