Merge pull request #77 from prmiles/dev_1.9.0

Update master branch to version 1.9.0

.readthedocs.yml

@@ -0,0 +1,2 @@
+python:
+  version: 3.6

CHANGELOG.rst

@@ -1,8 +1,18 @@
 Changelog
 =========
 
-v1.8.0 (June 28, 2019)
+v1.9.0 ()
 ---------
+- Added feature to results structure to store all parameters names, regardless of whether or not they are included in sampling.
+- Added mcmcplot package to requirements.  MCMCPlotting module is noted as deprecated.
+- Added new module for uncertainty propagation.  Aims to provide more flexible API for user to plot different combinations of credible and prediction intervals.
+- Added a plotting routine so that you can plot a 2-D interval in 3-D space.
+
+v1.8.0 (June 28, 2019)
+----------------------
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3261287.svg
+   :target: https://doi.org/10.5281/zenodo.3261287
+
 - Added acceptance rate display feature when calling chain statistics
 - User can specify `skip` or `maxpoints` in pairwise correlation and chain panel plots in order to thin chain.
 - User can request item definitions when calling `chainstats`.

README.rst

@@ -35,7 +35,7 @@ You can also clone the repository and run ``python  setup.py install``.
 Getting Started
 ===============
 
-- `Tutorial notebooks <https://nbviewer.jupyter.org/github/prmiles/pymcmcstat/tree/master/tutorials/index.ipynb>`_
+- `Tutorial notebooks <https://github.com/prmiles/pymcmcstat_examples>`_
 - `Documentation <http://pymcmcstat.readthedocs.io/>`_
 - `Release history <https://github.com/prmiles/pymcmcstat/blob/master/CHANGELOG.rst>`_
 - `Contributing guidelines <https://github.com/prmiles/pymcmcstat/blob/master/CONTRIBUTING.rst>`_

doc/source/pymcmcstat.rst

@@ -16,6 +16,14 @@ pymcmcstat.ParallelMCMC module
     :members:
     :undoc-members:
     :show-inheritance:
+
+pymcmcstat.propagation module
+------------------------------
+
+.. automodule:: pymcmcstat.propagation
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
 Subpackages
 -----------

pymcmcstat/__init__.py

@@ -1 +1,3 @@
-__version__ = "1.8.0"
+__version__ = "1.9.0"
+
+from mcmcplot import mcmcplot  # noqa, flake8 issue

pymcmcstat/plotting/MCMCPlotting.py

@@ -13,6 +13,8 @@
 from .utilities import generate_names, setup_plot_features, make_x_grid
 from .utilities import setup_subsample
 import warnings
+from deprecated import deprecated
+
 
 try:
     from statsmodels.nonparametric.kernel_density import KDEMultivariate
@@ -21,7 +23,13 @@
                       - plot_density_panel will not work. {}".format(e)))
 
 
+def deprecation(message):
+    warnings.warn(message, DeprecationWarning)
+
+
 # --------------------------------------------
+@deprecated(version='1.9.0',
+            reason='New function: "from pymcmcstat.mcmcplot import plot_density_panel"')
 def plot_density_panel(chains, names=None, hist_on=False, figsizeinches=None,
                        return_kde=False):
     '''
@@ -33,6 +41,7 @@ def plot_density_panel(chains, names=None, hist_on=False, figsizeinches=None,
         * **hist_on** (:py:class:`bool`): Flag to include histogram on density plot
         * **figsizeinches** (:py:class:`list`): Specify figure size in inches [Width, Height]
     '''
+    deprecation('Recommend using pymcmcstat.mcmcplot.plot_density_panel')
     nsimu, nparam = chains.shape  # number of rows, number of columns
     ns1, ns2, names, figsizeinches = setup_plot_features(
             nparam=nparam, names=names, figsizeinches=figsizeinches)
@@ -62,6 +71,8 @@ def plot_density_panel(chains, names=None, hist_on=False, figsizeinches=None,
 
 
 # --------------------------------------------
+@deprecated(version='1.9.0',
+            reason='New function: "from pymcmcstat.mcmcplot import plot_histogram_panel"')
 def plot_histogram_panel(chains, names=None, figsizeinches=None):
     """
     Plot histogram from each parameter's sampling history
@@ -90,6 +101,8 @@ def plot_histogram_panel(chains, names=None, figsizeinches=None):
 
 
 # --------------------------------------------
+@deprecated(version='1.9.0',
+            reason='New function:"from pymcmcstat.mcmcplot import plot_chain_panel"')
 def plot_chain_panel(chains, names=None, figsizeinches=None,
                      skip=1, maxpoints=500):
     """
@@ -128,6 +141,8 @@ def plot_chain_panel(chains, names=None, figsizeinches=None,
 
 
 # --------------------------------------------
+@deprecated(version='1.9.0',
+            reason='New function: "from pymcmcstat.mcmcplot import plot_pairwise_correlation_panel"')
 def plot_pairwise_correlation_panel(chains, names=None, figsizeinches=None,
                                     skip=1, maxpoints=500):
     """
@@ -176,6 +191,8 @@ def plot_pairwise_correlation_panel(chains, names=None, figsizeinches=None,
 
 
 # --------------------------------------------
+@deprecated(version='1.9.0',
+            reason='New function: "from pymcmcstat.mcmcplot import plot_chain_metrics"')
 def plot_chain_metrics(chain, name=None, figsizeinches=None):
     '''
     Plot chain metrics for individual chain