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This merge introduces v8.0.0 of MPAS-Atmosphere.

For a summary of significant changes, please see the annotation
of the v8.0.0 tag.
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mgduda committed Jun 16, 2023
2 parents 09bb84c + 49e9db7 commit 1d6ec7c
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613 changes: 535 additions & 78 deletions Makefile

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11 changes: 7 additions & 4 deletions README.md
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MPAS-v7.3
MPAS-v8.0.0
====

The Model for Prediction Across Scales (MPAS) is a collaborative project for
Expand Down Expand Up @@ -43,14 +43,17 @@ only described below the src directory.

MPAS-Model
├── src
│   ├── registry -- Code for building Registry.xml parser (Shared)
│   ├── driver -- Main driver for MPAS in stand-alone mode (Shared)
│   ├── external -- External software for MPAS (Shared)
│   ├── framework -- MPAS Framework (Includes DDT Descriptions, and shared routines. Shared)
│   ├── operators -- MPAS Opeartors (Includes Operators for MPAS meshes. Shared)
│   ├── inc -- Empty directory for include files that Registry generates (Shared)
│   ├── tools -- Empty directory for include files that Registry generates (Shared)
│   │  ├── registry -- Code for building Registry.xml parser (Shared)
│  │  └── input_gen -- Code for generating streams and namelist files (Shared)
│   └── core_* -- Individual model cores.
└────── testing_and_setup -- tools for setting up configurations and tests cases (Shared)
│   └── inc -- Empty directory for include files that Registry generates
├── testing_and_setup -- Tools for setting up configurations and test cases (Shared)
└── default_inputs -- Copies of default stream and namelists files (Shared)

Model cores are typically developed independently. For information about
building and running a particular core, please refer to that core's user's
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141 changes: 141 additions & 0 deletions azure-pipelines.yml
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trigger:
branches:
include:
- master
- develop
- ocean/develop
- lanice/develop
- ocean/coastal
tags:
include:
- '*'
pr:
branches:
include:
- master
- develop
- ocean/develop
- lanice/develop
- ocean/coastal

jobs:
- job:
displayName: docs
pool:
vmImage: 'ubuntu-16.04'
strategy:
matrix:
Python38:
python.version: '3.8'

steps:
- bash: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH

- bash: |
set -e
eval "$(conda shell.bash hook)"
conda config --add channels conda-forge
conda config --set channel_priority strict
displayName: Configure conda
- bash: |
set -e
eval "$(conda shell.bash hook)"
conda create -y -n docs python=$PYTHON_VERSION sphinx mock sphinx_rtd_theme m2r
displayName: Create docs environment
- bash: |
set -e
eval "$(conda shell.bash hook)"
conda activate docs
echo "source branch: $(Build.SourceBranch)"
echo "repository: $(Build.Repository.Name)"
tag=$(git describe --tags $(git rev-list --tags --max-count=1))
echo "tag: $tag"
REPO_PATH=$PWD
if [[ "$(Build.SourceBranch)" == refs/tags/* ]]; then
echo "this is a tag build"
export DOCS_VERSION="$tag"
deploy=True
run=True
elif [[ "$(Build.SourceBranch)" == refs/heads/* ]]; then
branch="$(Build.SourceBranchName)"
echo "this is a merge build of $branch"
deploy=True
elif [[ "$(Build.SourceBranch)" == refs/pull/*/merge ]]; then
branch="$(System.PullRequest.TargetBranch)"
echo "this is a pull request into $branch"
deploy=False
fi
if [ -n ${branch} ]; then
echo "This build is for branch $branch"
if [[ ${branch} == "master" ]]; then
export DOCS_VERSION="stable"
run=True
elif [[ ${branch} == "develop" ]]; then
export DOCS_VERSION="latest"
run=True
elif [[ ${branch} == "ocean/develop" ]]; then
export DOCS_VERSION="latest ocean"
run=True
elif [[ ${branch} == "ocean/coastal" ]]; then
export DOCS_VERSION="latest coastal"
run=True
elif [[ ${branch} == "landice/develop" ]]; then
export DOCS_VERSION="latest landice"
run=True
else
echo "We don't build docs for $branch"
deploy=False
run=False
fi
fi
if [[ "${run}" == "False" ]]; then
echo "Not building docs for branch ${branch}"
exit 0
fi
echo "Docs version: $DOCS_VERSION"
echo "Deploy to gh-pages? $deploy"
cd docs || exit 1
make html
cd "$REPO_PATH" || exit 1
if [[ "$deploy" == "False" ]]; then
exit 0
fi
PUBLICATION_BRANCH=gh-pages
DOCS_PATH="${DOCS_VERSION// /_}"
# Checkout the branch
pushd $HOME || exit 1
git clone --branch=$PUBLICATION_BRANCH https://$(GitHubToken)@github.com/$(Build.Repository.Name) publish
cd publish || exit 1
# Update pages
if [[ -d "$DOCS_PATH" ]]; then
git rm -rf "$DOCS_PATH" > /dev/null
fi
mkdir "$DOCS_PATH"
cp -r "$REPO_PATH"/docs/_build/html/* "$DOCS_PATH"
# Commit and push latest version
git add .
if git diff-index --quiet HEAD; then
echo "No changes in the docs."
else
git config --local user.name "Azure Pipelines"
git config --local user.email "[email protected]"
git commit -m "[skip ci] Update $DOCS_VERSION"
git push -fq origin $PUBLICATION_BRANCH
fi
popd || exit 1
displayName: build and deploy docs
20 changes: 20 additions & 0 deletions docs/Makefile
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# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = mpas_model
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)
182 changes: 182 additions & 0 deletions docs/conf.py
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# -*- coding: utf-8 -*-
#
# MPAS-Model documentation build configuration file, created by
# sphinx-quickstart on Sat Mar 25 14:39:11 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

import os

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.intersphinx',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon']

autosummary_generate = True

# Otherwise, the Return parameter list looks different from the Parameters list
napoleon_use_rtype = False
# Otherwise, the Attributes parameter list looks different from the Parameters
# list
napoleon_use_ivar = True

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
source_suffix = ['.rst']
# source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'MPAS-Model'
copyright = u'Copyright (c) 2013-2020, Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;' \
u'Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).'
author = u'Xylar Asay-Davis, Doug Jacobsen, Michael Duda, Mark Petersen, ' \
u'Matt Hoffman, Adridan Turner, Philip Wolfram'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
if 'DOCS_VERSION' in os.environ:
version = os.environ.get('DOCS_VERSION')
release = version
else:
# The short X.Y.Z version.
version = '7.0'
# The full version, including alpha/beta/rc tags.
release = '7.0'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
'design_docs/template.md']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False


# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#

# on_rtd is whether we are on readthedocs.org, this line of code grabbed from
# docs.readthedocs.org
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

if not on_rtd: # only import and set the theme if we're building docs locally
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']


# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'mpas_model_doc'


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',

# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',

# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',

# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'mpas_model.tex', u'MPAS-Model Documentation',
author, 'manual'),
]


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'mpas_model', u'MPAS-Model Documentation',
[author], 1)
]


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'mpas_model', u'MPAS-Model Documentation',
author, 'MPAS-Model', 'One line description of project.',
'Miscellaneous'),
]

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
'python': ('https://docs.python.org/', None),
'numpy': ('http://docs.scipy.org/doc/numpy/', None),
'xarray': ('http://xarray.pydata.org/en/stable/', None)}


github_doc_root = 'https://github.com/rtfd/recommonmark/tree/master/doc/'
23 changes: 23 additions & 0 deletions docs/index.rst
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MPAS-Model
==========

The Model for Prediction Across Scales (MPAS) is a collaborative project for
developing atmosphere, ocean, and other earth-system simulation components for
use in climate, regional climate, and weather studies. The primary development
partners are the climate modeling group at Los Alamos National Laboratory
(COSIM) and the National Center for Atmospheric Research. Both primary
partners are responsible for the MPAS framework, operators, and tools common to
the applications; LANL has primary responsibility for the ocean, sea-ice and
land-ice models, and NCAR has primary responsibility for the atmospheric model.

The MPAS framework facilitates the rapid development and prototyping of models
by providing infrastructure typically required by model developers, including
high-level data types, communication routines, and I/O routines. By using MPAS,
developers can leverage pre-existing code and focus more on development of

.. toctree::
:titlesonly:

ocean/index


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