Merge pull request #186 from GeoStat-Framework/doc_update

Doc update

CHANGELOG.md

@@ -2,6 +2,23 @@ Changelog
 =========
 
 
+Version 1.6.0
+-------------
+*April 04, 2021*
+
+**New features**
+
+* added Classification Kriging ([#165](https://github.com/GeoStat-Framework/PyKrige/pull/165), [#184](https://github.com/GeoStat-Framework/PyKrige/pull/184))
+* added wheels for Python 3.9 ([#175](https://github.com/GeoStat-Framework/PyKrige/pull/175))
+
+**Changes**
+
+* moved scikit-learn compat-class `Krige` to `pykrige.compat` ([#165](https://github.com/GeoStat-Framework/PyKrige/pull/165))
+* dropped Python 3.5 support ([#183](https://github.com/GeoStat-Framework/PyKrige/pull/183))
+* moved CI to GitHub-Actions ([#175](https://github.com/GeoStat-Framework/PyKrige/pull/175), [#183](https://github.com/GeoStat-Framework/PyKrige/pull/183))
+* Fixed Typo in `02_kriging3D.py` example ([#182](https://github.com/GeoStat-Framework/PyKrige/pull/182))
+
+
 Version 1.5.1
 -------------
 *August 20, 2020*

README.md

@@ -0,0 +1,118 @@
+# PyKrige
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3738604.svg)](https://doi.org/10.5281/zenodo.3738604)
+[![PyPI version](https://badge.fury.io/py/PyKrige.svg)](https://badge.fury.io/py/PyKrige)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/pykrige.svg)](https://anaconda.org/conda-forge/pykrige)
+[![Build Status](https://github.com/GeoStat-Framework/PyKrige/workflows/Continuous%20Integration/badge.svg?branch=develop)](https://github.com/GeoStat-Framework/PyKrige/actions)
+[![Coverage Status](https://coveralls.io/repos/github/GeoStat-Framework/PyKrige/badge.svg?branch=develop)](https://coveralls.io/github/GeoStat-Framework/PyKrige?branch=develop)
+[![Documentation Status](https://readthedocs.org/projects/pykrige/badge/?version=stable)](http://pykrige.readthedocs.io/en/stable/?badge=stable)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+
+<p align="center">
+<img src="https://github.com/GeoStat-Framework/GeoStat-Framework.github.io/raw/master/docs/source/pics/PyKrige_250.png" alt="PyKrige-LOGO" width="251px"/>
+</p>
+
+Kriging Toolkit for Python.
+
+## Purpose
+
+The code supports 2D and 3D ordinary and universal kriging. Standard
+variogram models (linear, power, spherical, gaussian, exponential) are
+built in, but custom variogram models can also be used. The 2D universal
+kriging code currently supports regional-linear, point-logarithmic, and
+external drift terms, while the 3D universal kriging code supports a
+regional-linear drift term in all three spatial dimensions. Both
+universal kriging classes also support generic 'specified' and
+'functional' drift capabilities. With the 'specified' drift capability,
+the user may manually specify the values of the drift(s) at each data
+point and all grid points. With the 'functional' drift capability, the
+user may provide callable function(s) of the spatial coordinates that
+define the drift(s). The package includes a module that contains
+functions that should be useful in working with ASCII grid files (`\*.asc`).
+
+See the documentation at <http://pykrige.readthedocs.io/> for more
+details and examples.
+
+## Installation
+
+PyKrige requires Python 3.5+ as well as numpy, scipy. It can be
+installed from PyPi with,
+
+``` bash
+pip install pykrige
+```
+
+scikit-learn is an optional dependency needed for parameter tuning and
+regression kriging. matplotlib is an optional dependency needed for
+plotting.
+
+If you use conda, PyKrige can be installed from the <span
+class="title-ref">conda-forge</span> channel with,
+
+``` bash
+conda install -c conda-forge pykrige
+```
+
+## Features
+
+### Kriging algorithms
+
+-   `OrdinaryKriging`: 2D ordinary kriging with estimated mean
+-   `UniversalKriging`: 2D universal kriging providing drift terms
+-   `OrdinaryKriging3D`: 3D ordinary kriging
+-   `UniversalKriging3D`: 3D universal kriging
+-   `RegressionKriging`: An implementation of Regression-Kriging
+-   `ClassificationKriging`: An implementation of Simplicial Indicator
+    Kriging
+
+### Wrappers
+
+-   `rk.Krige`: A scikit-learn wrapper class for Ordinary and Universal
+    Kriging
+
+### Tools
+
+-   `kriging_tools.write_asc_grid`: Writes gridded data to ASCII grid
+    file (`\*.asc`)
+-   `kriging_tools.read_asc_grid`: Reads ASCII grid file (`\*.asc`)
+
+### Kriging Parameters Tuning
+
+A scikit-learn compatible API for parameter tuning by cross-validation
+is exposed in
+[sklearn.model\_selection.GridSearchCV](http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.GridSearchCV.html).
+See the [Krige
+CV](http://pykrige.readthedocs.io/en/latest/examples/08_krige_cv.html#sphx-glr-examples-08-krige-cv-py)
+example for a more practical illustration.
+
+### Regression Kriging
+
+[Regression kriging](https://en.wikipedia.org/wiki/Regression-Kriging)
+can be performed with
+[pykrige.rk.RegressionKriging](http://pykrige.readthedocs.io/en/latest/examples/07_regression_kriging2d.html).
+This class takes as parameters a scikit-learn regression model, and
+details of either either the `OrdinaryKriging` or the `UniversalKriging`
+class, and performs a correction steps on the ML regression prediction.
+
+A demonstration of the regression kriging is provided in the
+[corresponding
+example](http://pykrige.readthedocs.io/en/latest/examples/07_regression_kriging2d.html#sphx-glr-examples-07-regression-kriging2d-py).
+
+### Classification Kriging
+
+[Simplifical Indicator
+kriging](https://www.sciencedirect.com/science/article/abs/pii/S1002070508600254)
+can be performed with
+[pykrige.rk.ClassificationKriging](http://pykrige.readthedocs.io/en/latest/examples/10_classification_kriging2d.html).
+This class takes as parameters a scikit-learn classification model, and
+details of either the `OrdinaryKriging` or the `UniversalKriging` class,
+and performs a correction steps on the ML classification prediction.
+
+A demonstration of the classification kriging is provided in the
+[corresponding
+example](http://pykrige.readthedocs.io/en/latest/examples/10_classification_kriging2d.html#sphx-glr-examples-10-classification-kriging2d-py).
+
+## License
+
+PyKrige uses the BSD 3-Clause License.

docs/requirements_doc.txt

@@ -2,7 +2,7 @@ scikit-learn>=0.19
 gstools>=1.1.1
 sphinx
 pillow
-recommonmark
 sphinx_rtd_theme
 sphinxcontrib-napoleon
 sphinx-gallery
+m2r2

docs/source/changelog.rst

@@ -1,2 +1,2 @@
 
-.. include:: ../../CHANGELOG.md
+.. mdinclude:: ../../CHANGELOG.md

docs/source/conf.py

@@ -48,7 +48,7 @@
     "sphinxcontrib.napoleon",
     "sphinx_gallery.gen_gallery",
     "sphinx.ext.linkcode",
-    "recommonmark",
+    "m2r2",
 ]
 
 
@@ -244,6 +244,8 @@
 
 # -- Options for LaTeX output ---------------------------------------------
 
+latex_logo = "pics/PyKrige_150.png"
+
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #'papersize': 'letterpaper',

docs/source/index.rst

@@ -1,2 +1,2 @@
 
-.. include:: ../../README.rst
+.. mdinclude:: ../../README.md

setup.py

@@ -35,7 +35,7 @@
 
 # setup #######################################################################
 
-with open(os.path.join(HERE, "README.rst"), encoding="utf-8") as f:
+with open(os.path.join(HERE, "README.md"), encoding="utf-8") as f:
     README = f.read()
 with open(os.path.join(HERE, "requirements.txt"), encoding="utf-8") as f:
     REQ = f.read().splitlines()
@@ -78,7 +78,7 @@
     name="PyKrige",
     description=DOCLINE,
     long_description=README,
-    long_description_content_type="text/x-rst",
+    long_description_content_type="text/markdown",
     author="Benjamin S. Murphy",
     author_email="[email protected]",
     maintainer="Sebastian Mueller, Roman Yurchak",