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Merge branch 'release-v8.0.0'
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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‎Makefile

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‎README.md

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MPAS-v7.3
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MPAS-v8.0.0
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====
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The Model for Prediction Across Scales (MPAS) is a collaborative project for
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MPAS-Model
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├── src
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│   ├── registry -- Code for building Registry.xml parser (Shared)
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│   ├── driver -- Main driver for MPAS in stand-alone mode (Shared)
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│   ├── external -- External software for MPAS (Shared)
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│   ├── framework -- MPAS Framework (Includes DDT Descriptions, and shared routines. Shared)
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│   ├── operators -- MPAS Opeartors (Includes Operators for MPAS meshes. Shared)
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│   ├── inc -- Empty directory for include files that Registry generates (Shared)
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│   ├── tools -- Empty directory for include files that Registry generates (Shared)
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│   │  ├── registry -- Code for building Registry.xml parser (Shared)
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│  │  └── input_gen -- Code for generating streams and namelist files (Shared)
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│   └── core_* -- Individual model cores.
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└────── testing_and_setup -- tools for setting up configurations and tests cases (Shared)
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│   └── inc -- Empty directory for include files that Registry generates
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├── testing_and_setup -- Tools for setting up configurations and test cases (Shared)
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└── default_inputs -- Copies of default stream and namelists files (Shared)
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Model cores are typically developed independently. For information about
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building and running a particular core, please refer to that core's user's

‎azure-pipelines.yml

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trigger:
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branches:
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include:
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- master
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- develop
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- ocean/develop
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- lanice/develop
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- ocean/coastal
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tags:
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include:
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- '*'
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pr:
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branches:
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include:
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- master
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- develop
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- ocean/develop
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- lanice/develop
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- ocean/coastal
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jobs:
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- job:
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displayName: docs
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pool:
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vmImage: 'ubuntu-16.04'
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strategy:
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matrix:
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Python38:
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python.version: '3.8'
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steps:
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- bash: echo "##vso[task.prependpath]$CONDA/bin"
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displayName: Add conda to PATH
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- bash: |
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set -e
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eval "$(conda shell.bash hook)"
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conda config --add channels conda-forge
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conda config --set channel_priority strict
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displayName: Configure conda
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- bash: |
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set -e
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eval "$(conda shell.bash hook)"
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conda create -y -n docs python=$PYTHON_VERSION sphinx mock sphinx_rtd_theme m2r
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displayName: Create docs environment
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- bash: |
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set -e
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eval "$(conda shell.bash hook)"
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conda activate docs
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echo "source branch: $(Build.SourceBranch)"
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echo "repository: $(Build.Repository.Name)"
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tag=$(git describe --tags $(git rev-list --tags --max-count=1))
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echo "tag: $tag"
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REPO_PATH=$PWD
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if [[ "$(Build.SourceBranch)" == refs/tags/* ]]; then
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echo "this is a tag build"
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export DOCS_VERSION="$tag"
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deploy=True
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run=True
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elif [[ "$(Build.SourceBranch)" == refs/heads/* ]]; then
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branch="$(Build.SourceBranchName)"
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echo "this is a merge build of $branch"
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deploy=True
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elif [[ "$(Build.SourceBranch)" == refs/pull/*/merge ]]; then
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branch="$(System.PullRequest.TargetBranch)"
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echo "this is a pull request into $branch"
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deploy=False
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fi
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if [ -n ${branch} ]; then
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echo "This build is for branch $branch"
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if [[ ${branch} == "master" ]]; then
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export DOCS_VERSION="stable"
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run=True
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elif [[ ${branch} == "develop" ]]; then
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export DOCS_VERSION="latest"
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run=True
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elif [[ ${branch} == "ocean/develop" ]]; then
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export DOCS_VERSION="latest ocean"
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run=True
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elif [[ ${branch} == "ocean/coastal" ]]; then
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export DOCS_VERSION="latest coastal"
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run=True
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elif [[ ${branch} == "landice/develop" ]]; then
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export DOCS_VERSION="latest landice"
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run=True
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else
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echo "We don't build docs for $branch"
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deploy=False
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run=False
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fi
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fi
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if [[ "${run}" == "False" ]]; then
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echo "Not building docs for branch ${branch}"
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exit 0
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fi
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echo "Docs version: $DOCS_VERSION"
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echo "Deploy to gh-pages? $deploy"
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cd docs || exit 1
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make html
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cd "$REPO_PATH" || exit 1
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if [[ "$deploy" == "False" ]]; then
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exit 0
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fi
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PUBLICATION_BRANCH=gh-pages
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DOCS_PATH="${DOCS_VERSION// /_}"
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# Checkout the branch
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pushd $HOME || exit 1
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git clone --branch=$PUBLICATION_BRANCH https://$(GitHubToken)@github.com/$(Build.Repository.Name) publish
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cd publish || exit 1
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# Update pages
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if [[ -d "$DOCS_PATH" ]]; then
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git rm -rf "$DOCS_PATH" > /dev/null
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fi
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mkdir "$DOCS_PATH"
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cp -r "$REPO_PATH"/docs/_build/html/* "$DOCS_PATH"
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# Commit and push latest version
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git add .
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if git diff-index --quiet HEAD; then
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echo "No changes in the docs."
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else
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git config --local user.name "Azure Pipelines"
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git config --local user.email "[email protected]"
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git commit -m "[skip ci] Update $DOCS_VERSION"
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git push -fq origin $PUBLICATION_BRANCH
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fi
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popd || exit 1
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displayName: build and deploy docs
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‎docs/Makefile

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

‎docs/conf.py

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# -*- coding: utf-8 -*-
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#
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# MPAS-Model documentation build configuration file, created by
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# sphinx-quickstart on Sat Mar 25 14:39:11 2017.
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#
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# This file is execfile()d with the current directory set to its
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# containing dir.
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#
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# Note that not all possible configuration values are present in this
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# autogenerated file.
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#
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# All configuration values have a default; values that are commented out
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# serve to show the default.
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import os
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# -- General configuration ------------------------------------------------
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# If your documentation needs a minimal Sphinx version, state it here.
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#
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# needs_sphinx = '1.0'
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ['sphinx.ext.autodoc',
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'sphinx.ext.autosummary',
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'sphinx.ext.intersphinx',
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'sphinx.ext.mathjax',
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'sphinx.ext.viewcode',
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'sphinx.ext.napoleon']
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autosummary_generate = True
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# Otherwise, the Return parameter list looks different from the Parameters list
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napoleon_use_rtype = False
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# Otherwise, the Attributes parameter list looks different from the Parameters
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# list
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napoleon_use_ivar = True
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# The suffix(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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#
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source_suffix = ['.rst']
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# source_suffix = '.rst'
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# The master toctree document.
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master_doc = 'index'
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# General information about the project.
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project = u'MPAS-Model'
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copyright = u'Copyright (c) 2013-2020, Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;' \
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u'Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).'
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author = u'Xylar Asay-Davis, Doug Jacobsen, Michael Duda, Mark Petersen, ' \
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u'Matt Hoffman, Adridan Turner, Philip Wolfram'
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# built documents.
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if 'DOCS_VERSION' in os.environ:
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version = os.environ.get('DOCS_VERSION')
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release = version
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else:
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# The short X.Y.Z version.
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version = '7.0'
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# The full version, including alpha/beta/rc tags.
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release = '7.0'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This patterns also effect to html_static_path and html_extra_path
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
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'design_docs/template.md']
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = 'sphinx'
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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = False
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# -- Options for HTML output ----------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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# on_rtd is whether we are on readthedocs.org, this line of code grabbed from
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# docs.readthedocs.org
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on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
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if not on_rtd: # only import and set the theme if we're building docs locally
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import sphinx_rtd_theme
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html_theme = 'sphinx_rtd_theme'
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html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
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# Theme options are theme-specific and customize the look and feel of a theme
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# further. For a list of options available for each theme, see the
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# documentation.
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#
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# html_theme_options = {}
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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# -- Options for HTMLHelp output ------------------------------------------
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'mpas_model_doc'
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# -- Options for LaTeX output ---------------------------------------------
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latex_elements = {
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# The paper size ('letterpaper' or 'a4paper').
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#
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# 'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#
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# 'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#
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# 'preamble': '',
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# Latex figure (float) alignment
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#
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# 'figure_align': 'htbp',
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}
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title,
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# author, documentclass [howto, manual, or own class]).
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latex_documents = [
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(master_doc, 'mpas_model.tex', u'MPAS-Model Documentation',
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author, 'manual'),
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]
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# -- Options for manual page output ---------------------------------------
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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(master_doc, 'mpas_model', u'MPAS-Model Documentation',
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[author], 1)
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]
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# -- Options for Texinfo output -------------------------------------------
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# Grouping the document tree into Texinfo files. List of tuples
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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(master_doc, 'mpas_model', u'MPAS-Model Documentation',
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author, 'MPAS-Model', 'One line description of project.',
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'Miscellaneous'),
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]
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {
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'python': ('https://docs.python.org/', None),
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'numpy': ('http://docs.scipy.org/doc/numpy/', None),
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'xarray': ('http://xarray.pydata.org/en/stable/', None)}
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github_doc_root = 'https://github.com/rtfd/recommonmark/tree/master/doc/'

‎docs/index.rst

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MPAS-Model
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==========
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The Model for Prediction Across Scales (MPAS) is a collaborative project for
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developing atmosphere, ocean, and other earth-system simulation components for
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use in climate, regional climate, and weather studies. The primary development
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partners are the climate modeling group at Los Alamos National Laboratory
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(COSIM) and the National Center for Atmospheric Research. Both primary
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partners are responsible for the MPAS framework, operators, and tools common to
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the applications; LANL has primary responsibility for the ocean, sea-ice and
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land-ice models, and NCAR has primary responsibility for the atmospheric model.
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The MPAS framework facilitates the rapid development and prototyping of models
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by providing infrastructure typically required by model developers, including
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high-level data types, communication routines, and I/O routines. By using MPAS,
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developers can leverage pre-existing code and focus more on development of
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.. toctree::
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:titlesonly:
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ocean/index
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