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.

README.md

@@ -1,4 +1,4 @@
-MPAS-v7.3
+MPAS-v8.0.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for
@@ -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

azure-pipelines.yml

@@ -0,0 +1,141 @@
+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 "azuredevops@microsoft.com"
+        git commit -m "[skip ci] Update $DOCS_VERSION"
+        git push -fq origin $PUBLICATION_BRANCH
+      fi
+      popd || exit 1
+    displayName: build and deploy docs
+

docs/Makefile

@@ -0,0 +1,20 @@
+# 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)

docs/conf.py

@@ -0,0 +1,182 @@
+# -*- 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/'

docs/index.rst

@@ -0,0 +1,23 @@
+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
+
+