Squashed '.lib/git-fleximod/' content from commit 69a5dc5

git-subtree-dir: .lib/git-fleximod
git-subtree-split: 69a5dc5

.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]

.pre-commit-config.yaml

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+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

License

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+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.

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.

doc/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "git-fleximod"
+author = "Jim Edwards <[email protected]>"
+release = "0.4.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx_argparse_cli"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["_static"]

doc/index.rst

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+.. git-fleximod documentation master file, created by
+   sphinx-quickstart on Sat Feb  3 12:02:22 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to git-fleximod's documentation!
+========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+.. module:: sphinxcontrib.autoprogram
+.. sphinx_argparse_cli::
+   :module: git_fleximod.cli
+   :func: get_parser
+   :prog: git-fleximod
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

escomp_install

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+#!/usr/bin/env python
+# updates git-fleximod in an ESCOMP model
+# this script should be run from the model root directory, it expects
+# git-fleximod to already be installed with the script in bin
+# and the classes in lib/python/site-packages
+import sys
+import shutil
+import os
+
+from glob import iglob
+
+fleximod_root = sys.argv[1]
+fleximod_path = os.path.join(fleximod_root,"src","git-fleximod")
+if os.path.isfile(fleximod_path):
+   with open(fleximod_path,"r") as f:
+        fleximod = f.readlines()
+   with open(os.path.join(".","bin","git-fleximod"),"w") as f:
+        for line in fleximod:
+            f.write(line)
+            if "import argparse" in line:
+               f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n')
+
+   for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")):
+       shutil.copy(file,
+        os.path.join("lib","python","site-packages","fleximod",os.path.basename(file)))