Merge pull request #1 from xylar/move_repo

Move repo from xylar/pyremap to MPAS-Dev

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# 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

.pep8speaks.yml

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+pycodestyle:
+    max-line-length: 80

LICENSE

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+This software is open source software available under the BSD-3 license.
+
+Copyright (c) 2019 Triad National Security, LLC. All rights reserved.
+Copyright (c) 2019 Lawrence Livermore National Security, LLC. All rights reserved.
+Copyright (c) 2019 UT-Battelle, LLC. All rights reserved.
+
+
+Copyright (c) 2019 Triad National Security, LLC. This program was produced
+under U.S. Government contract 89233218CNA000001 for Los Alamos National
+Laboratory (LANL), which is operated by Triad National Security, LLC for the
+U.S. Department of Energy/National Nuclear Security Administration. All rights
+in the program are reserved by Triad National Security, LLC, and the U.S.
+Department of Energy/National Nuclear Security Administration. The Government
+is granted for itself and others acting on its behalf a nonexclusive, paid-up,
+irrevocable worldwide license in this material to reproduce, prepare derivative
+works, distribute copies to the public, perform publicly and display publicly,
+and to permit others to do so.
+
+Copyright (c) 2019 Lawrence Livermore National Security, LLC. This work was
+produced under the auspices of the U.S. Department of Energy by Lawrence
+Livermore National Laboratory under Contract DE-AC52-07NA27344. This work was
+prepared as an account of work sponsored by an agency of the United States
+Government. Neither the United States Government nor Lawrence Livermore
+National Security, LLC, nor any of their employees makes any warranty,
+expressed or implied, or assumes any legal liability or responsibility for the
+accuracy, completeness, or usefulness of any information, apparatus, product,
+or process disclosed, or represents that its use would not infringe privately
+owned rights. Reference herein to any specific commercial product, process, or
+service by trade name, trademark, manufacturer, or otherwise does not
+necessarily constitute or imply its endorsement, recommendation, or favoring by
+the United States Government or Lawrence Livermore National Security, LLC. The
+views and opinions of authors expressed herein do not necessarily state or
+reflect those of the United States Government or Lawrence Livermore National
+Security, LLC, and shall not be used for advertising or product endorsement
+purposes.
+
+Copyright 2019 UT-Battelle. LLC. This technology acquired under license from
+UT-Battelle, LLC, the management and operating contractor of the Oak Ridge
+National Laboratory acting on behalf of the U.S. Department of Energy under
+Contract No. DE-AC05-00OR22725. The United States Government and UT-Battelle,
+LLC make no representations and disclaim all warranties, both expressed and
+implied.  There are no express or implied warranties of merchantability or
+fitness for a particular purpose, or that the use of the software will not
+infringe any patent, copyright, trademark, or other proprietary rights, or that
+the software will accomplish the intended results or that the software or its
+use will not result in injury or damage.  The user assumes responsibility for
+all liabilities, penalties, fines, claims, causes of action, and costs and
+expenses, caused by, resulting from or arising out of, in whole or in part the
+use, storage or disposal of the software.
+
+Additionally, redistribution and use in source and binary forms, with or
+without modification, are permitted provided that the following conditions are
+met:
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* 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.
+* Neither the name of Los Alamos National Security, LLC, Los Alamos National
+  Laboratory, LANL, the U.S. Government, nor the names of its contributors may
+  be used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC 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 LOS ALAMOS NATIONAL SECURITY, LLC 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.

README.md

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-# pyremap
+# pyremap
+[![Documentation Status](http://readthedocs.org/projects/pyremap/badge/?version=latest)](http://pyremap.readthedocs.io/en/latest/?badge=latest)
+
+Python remapping tools for climate and earth system models.
+
+## Documentation
+
+[http://pyremap.readthedocs.io](http://pyremap.readthedocs.io)
+
+## Installation
+
+To use the latest version for developers, you will need to set up a conda
+environment with the following packages:
+
+ * python >= 3.6
+ * numpy
+ * scipy
+ * netcdf4
+ * xarray >= 0.10.0
+ * dask
+ * nco >= 4.8.1
+ * pyproj
+
+These can be installed via the conda command:
+```
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+conda create -n pyremap python=3.7 numpy scipy netcdf4 "xarray>=0.10.0" dask \
+    "nco>=4.8.1" pyproj
+conda activate pyremap
+```
+
+Then, get the code from:
+[https://github.com/xylar/pyremap](https://github.com/xylar/pyremap)
+
+
+## Examples
+
+```
+cd examples
+```
+The simplest way to make pyremap available is:
+```
+ln -s ../pyremap
+```
+First, make mapping files for a lat-lon grid, and test it out by remapping
+temperature from the example file:
+```
+wget https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/mpas-o/oQU240/ocean.QU.240km.151209.nc
+./make_mpas_to_lat_lon_mapping.py
+```
+You should now see the mapping file:
+```
+map_oQU240_to_0.5x0.5degree.nc
+```
+as well as the input file (an initial condition for the MPAS-Ocean model) and
+an example of temperature from the initial condition remapped to the new grid.
+```
+ocean.QU.240km.151209.nc
+temp_0.5x0.5degree.nc
+```
+
+Second, let's try the same but to an Antarctic stereographic grid:
+```
+./make_mpas_to_Antarctic_stereo_mapping.py
+```
+Now, there's a new mapping file and example output file:
+```
+map_oQU240_to_6000.0x6000.0km_10.0km_Antarctic_stereo.nc
+temp_6000.0x6000.0km_10.0km_Antarctic_stereo.nc
+```
+
+Finally, let's remap the temperature on the Antarctic grid to a lower
+resolution Antarctic grid:
+```
+./remap_stereographic.py -i temp_6000.0x6000.0km_10.0km_Antarctic_stereo.nc \
+    -o temp_6000.0x6000.0km_20.0km_Antarctic_stereo.nc -r 20
+```
+This created another mapping file and an output file:
+```
+map_6000x6000km_10km_Antarctic_stereo_to_6000x6000km_20.0km_Antarctic_stereo.nc
+temp_6000.0x6000.0km_20.0km_Antarctic_stereo.nc
+```

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    = pyremap
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -rf generated
+	@$(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)

docs/api.rst

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+#############
+API reference
+#############
+
+This page provides an auto-generated summary of the pyremap API. 
+
+Mesh Descriptors
+================
+
+.. currentmodule:: pyremap.descriptor
+
+.. autosummary::
+   :toctree: generated/
+
+   get_lat_lon_descriptor
+   MpasMeshDescriptor
+   LatLonGridDescriptor
+   LatLon2DGridDescriptor
+   ProjectionGridDescriptor
+   PointCollectionDescriptor
+
+Remapping
+=========
+
+.. currentmodule:: pyremap.remapper
+
+.. autosummary::
+   :toctree: generated/
+
+   Remapper
+
+
+Polar projections
+=================
+
+.. currentmodule:: pyremap.polar
+
+.. autosummary::
+   :toctree: generated/
+
+   get_arctic_stereographic_projection
+   get_antarctic_stereographic_projection
+   get_polar_descriptor_from_file
+   get_polar_descriptor
+   to_polar
+   from_polar
+