Merge pull request #248 from xylar/mesh_tools_conda_package

conda package for MPAS tools 

This package is intended to include all the tools needed to run run COMPASS test cases and other typical mesh creation workflows.  This includes:
* the mesh conversion tools (#243)
* a python interface to the mesh conversion tools
* the planar hex creation tool (#246)
* a modified version of the mesh translation tool (python 3 compatible and callable as a function as well as a script
* 4 land-ice mesh tools (updated for python 3)
* 3 ocean coastal modification scripts (now available as functions and updated for python 3)
* add a copy of the MPAS-Model license (a license is required for conda-forge packages)
* a starting point for documentation

Author: xylar

.gitignore

@@ -9,3 +9,95 @@
 *.png
 
 # Each tool should also have it's own .gitignore file that ignores the build files for that tool.
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+.DS_Store

LICENSE

@@ -0,0 +1,39 @@
+Copyright (c) 2013-2018,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
+Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).
+
+All rights reserved. 
+
+LANS is the operator of the Los Alamos National Laboratory under Contract No.
+DE-AC52-06NA25396 with the U.S. Department of Energy.  UCAR manages the National
+Center for Atmospheric Research under Cooperative Agreement ATM-0753581 with the
+National Science Foundation.  The U.S. Government has rights to use, reproduce,
+and distribute this software.  NO WARRANTY, EXPRESS OR IMPLIED IS OFFERED BY
+LANS, UCAR OR THE GOVERNMENT AND NONE OF THEM ASSUME ANY LIABILITY FOR THE USE
+OF THIS SOFTWARE.  If software is modified to produce derivative works, such
+modified software should be clearly marked, so as not to confuse it with the
+version available from LANS and UCAR.
+
+Additionally, redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1) Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2) Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+3) None of the names of LANS, UCAR or the names of its contributors, if any, may
+be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

conda_package/docs/Makefile

@@ -0,0 +1,24 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = mpas_tools
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -rf *obs_table.rst generated obs
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(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)

conda_package/docs/api.rst

@@ -0,0 +1,55 @@
+#############
+API reference
+#############
+
+This page provides an auto-generated summary of the MPAS mesh-tools API. For
+more details and examples, refer to the relevant chapters in the main part of
+the documentation.
+
+MPAS mesh tools
+===============
+
+.. currentmodule:: mpas_tools.planar_hex
+
+.. autosummary::
+   :toctree: generated/
+
+   make_periodic_planar_hex_mesh
+
+.. currentmodule:: mpas_tools.translate
+
+.. autosummary::
+   :toctree: generated/
+
+   translate
+
+
+.. currentmodule:: mpas_tools.conversion
+
+.. autosummary::
+   :toctree: generated/
+
+   convert
+   cull
+   mask
+
+
+.. currentmodule:: mpas_tools.io
+
+.. autosummary::
+   :toctree: generated/
+
+   write_netcdf
+
+
+Ocean Tools
+===========
+
+.. currentmodule:: mpas_tools.ocean.coastline_alteration
+
+.. autosummary::
+   :toctree: generated/
+
+   add_critical_land_blockages
+   widen_transect_edge_masks
+

conda_package/docs/conf.py

@@ -0,0 +1,180 @@
+# -*- coding: utf-8 -*-
+#
+# mpas_tools 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
+import mpas_tools
+
+# -- 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',
+              'numpydoc']
+
+autosummary_generate = True
+
+numpydoc_class_members_toctree = True
+numpydoc_show_class_members = False
+
+# 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_tools'
+copyright = u'This software is open source software available under the BSD-3' \
+            u'license. Copyright (c) 2019 Triad National Security, LLC. ' \
+            u'All rights reserved. Copyright (c) 2018 Lawrence Livermore ' \
+            u'National Security, LLC. All rights reserved. Copyright (c) ' \
+            u'2018 UT-Battelle, LLC. All rights reserved.'
+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.
+#
+# The short X.Y version.
+version = u'0.0.1'
+# The full version, including alpha/beta/rc tags.
+release = u'0.0.1'
+
+# 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_tools_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_tools.tex', u'mpas_tools 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_tools', u'mpas_tools 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_tools', u'mpas_tools Documentation',
+     author, 'mpas_tools', '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/'