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first round of doc additions
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Joseph Hamman committed Oct 10, 2019
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19 changes: 19 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
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)
38 changes: 38 additions & 0 deletions docs/api.rst
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.. currentmodule:: xsd.pointwise_models

#############
API reference
#############

This page provides an auto-generated summary of xsd's API. For more details
and examples, refer to the relevant chapters in the main part of the
documentation.

Pointwise methods
=================

Xarray Wrappers
~~~~~~~~~~~~~~~

.. autosummary::
:toctree: generated/

PointWiseDownscaler

Linear Models
~~~~~~~~~~~~~

.. autosummary::
:toctree: generated/

BcsdPrecipitation
BcsdTemperature

Transformers
~~~~~~~~~~~~

.. autosummary::
:toctree: generated/

LinearTrendTransformer
QuantileMapper
192 changes: 192 additions & 0 deletions docs/conf.py
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# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------
from pkg_resources import get_distribution
import xsd

project = 'xsd'
copyright = '2019, Joe Hamman'
author = 'Joe Hamman'

release = get_distribution('xsd').version
# for example take major/minor
version = '.'.join(release.split('.')[:2])

# -- 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.intersphinx',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.autosummary'
]

# 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', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# 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 pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

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


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

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

# 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']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


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

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


# -- 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, 'xsd.tex', 'xsd Documentation',
'Joe Hamman', '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, 'xsd', 'xsd 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, 'xsd', 'xsd Documentation',
author, 'xsd', 'Statistical Downscaling in Python',
'Miscellaneous'),
]


# -- Options for Epub output -------------------------------------------------

# Bibliographic Dublin Core info.
epub_title = project

# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''

# A unique identification for the text.
#
# epub_uid = ''

# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']


# -- Extension configuration -------------------------------------------------

# -- Options for intersphinx extension ---------------------------------------

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
"python": ("https://docs.python.org/3/", None),
"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
"numpy": ("https://docs.scipy.org/doc/numpy/", None),
"xarray": ("http://xarray.pydata.org/en/stable/", None),
"scikit-learn": ("https://scikit-learn.org/stable/", None),
}
21 changes: 21 additions & 0 deletions docs/index.rst
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.. xsd documentation master file, created by
sphinx-quickstart on Wed Oct 9 13:59:33 2019.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to xsd's documentation!
===============================

.. toctree::
:maxdepth: 2
:caption: Contents:

roadmap
api

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
120 changes: 120 additions & 0 deletions docs/roadmap.rst
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.. _roadmap:

Development Roadmap
===================

Author: Joe Hamman
Date:September 15, 2019

Background and scope
--------------------

`xsd` is a toolkit for statistical downscaling usising Xarray. It is meant to
support the development of new and existing downscaling methods in a common
framework. It implements a train/predict API that accepts Xarray objects,
similiar to Python's Scikit-Learn, for building a range of downscaling models.
For example, implementing a BCSD workflow may look something like this:

.. code-block:: Python
from xsd.pointwise_models import PointWiseDownscaler
from xsd.models.bcsd import BCSDTemperature, bcsd_disaggregator
# da_temp_train: xarray.DataArray (monthly)
# da_temp_obs: xarray.DataArray (monthly)
# da_temp_obs_daily: xarray.DataArray (daily)
# da_temp_predict: xarray.DataArray (monthly)
# create a model
bcsd_model = PointWiseDownscaler(BCSDTemperature(), dim='time')
# train the model
bcsd_model.train(da_temp_train, da_temp_obs)
# predict with the model (downscaled_temp: xr.DataArray)
downscaled_temp = bcsd_model.predict(da_temp_predict)
# disaggregate the downscaled data (final: xr.DataArray)
final = bcsd_disaggregator(downscaled_temp, da_temp_obs_daily)
We are currently envisioning the project having three componenets (described
in the components section below). While we haven't started work on the deep
learning models component, this is certainly a central motivation to this
package and I am looking forward to starting on this work soon.

Principles
----------

- Open - aim to take the sausage making out downscaling; open-source methods,
comparable, extensible
- Scalable - plug into existing frameworks (e.g. dask/pangeo) to scale up,
allow for use a single points to scale down
- Portable - unopionated when it comes to compute platform
- Tested - Rigourously tested, both on the computational and scientific
implementation

Components
----------

1. `pointwise_models`: a collection of linear models that are intended to be
applied point-by-point. These may be sklearn Pipelines or custom sklearn-like
models (e.g. BCSDTemperature).
2. `global_models`: (not implemented) concept space for deep learning-based
models.
3. `metrics`: (not implemented) concept space for a benchmarking suite

Models
------

XSD should provide a collection of a common set of downscaling models and the
building blocks to construct new models. As a starter, I intend to implement
the following models:

Pointwise models
~~~~~~~~~~~~~~~~

1. BCSD_[Temperature, Precipitation]: Wood et al 2002
2. ARRM: Stoner et al 2012
3. Delta Method
4. Hybrid Delta Method
5. GARD: https://github.com/NCAR/GARD
6. ?

Other methods, like LOCA, MACA, BCCA, etc, should also be possible.

Global models
~~~~~~~~~~~~~

This category of methods is really what is motivating the development of this
package. We've seen some early work from TJ Vandal in this area but there is
more work to be done. For now, I'll just jot down what a possible API might
look like:

.. code-block:: Python
from xsd.global_models import GlobalDownscaler
from xsd.global_models.deepsd import DeepSD
# ...
# create a model
model = GlobalDownscaler(DeepSD())
# train the model
model.train(da_temp_train, da_temp_obs)
# predict with the model (downscaled_temp: xr.DataArray)
downscaled_temp = model.predict(da_temp_predict)
Dependencies
------------

- Core: Xarray, Pandas, Dask, Scikit-learn, Numpy, Scipy
- Optional: Statsmodels, Keras, PyTorch, Tensorflow, etc.

Related projects
----------------

- FUDGE: https://github.com/NOAA-GFDL/FUDGE
- GARD: https://github.com/NCAR/GARD
- DeepSD: https://github.com/tjvandal/deepsd
2 changes: 2 additions & 0 deletions pyproject.toml
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[build-system]
requires = ["setuptools>=30.3.0", "wheel", "setuptools_scm"]
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