Updates to documentation

Author: williamjameshandley

MANIFEST.in

@@ -1 +1,2 @@
 include README.rst
+recursive-include fgivenx/test/baseline_images/ *.pdf

README.rst

@@ -3,7 +3,7 @@ fgivenx: Functional Posterior Plotter
 =====================================
 :fgivenx:  Functional Posterior Plotter 
 :Author: Will Handley
-:Version: 2.1.10
+:Version: 2.1.11
 :Homepage: https://github.com/williamjameshandley/fgivenx
 :Documentation: http://fgivenx.readthedocs.io/
 
@@ -285,9 +285,10 @@ Pull requests are very welcome. Note that if you are going to propose drastic
 changes, be sure to open an issue for discussion first, to make sure that your
 PR will be accepted before you spend effort coding it.
 
-.. |image0| image:: https://github.com/williamjameshandley/fgivenx/blob/master/plot.png
-.. |image1| image:: https://github.com/williamjameshandley/fgivenx/blob/master/planck.png
+.. |image0| image:: https://raw.githubusercontent.com/williamjameshandley/fgivenx/master/plot.png
+.. |image1| image:: https://raw.githubusercontent.com/williamjameshandley/fgivenx/master/planck.png 
 
 Changelog
 =========
+:v2.1.11: Documentation upgrades
 :v2.1.10: Added changelog

docs/source/conf.py

@@ -47,14 +47,11 @@ def get_version(short=False):
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
+    'sphinx.ext.imgconverter',
     'numpydoc',
 ]
 

docs/source/fgivenx.rst

@@ -1,6 +1,14 @@
 fgivenx package
 ===============
 
+Module contents
+---------------
+
+.. automodule:: fgivenx
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 Submodules
 ----------
 
@@ -59,12 +67,3 @@ fgivenx.samples module
     :members:
     :undoc-members:
     :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: fgivenx
-    :members:
-    :undoc-members:
-    :show-inheritance:

fgivenx/__init__.py

@@ -1,2 +1,29 @@
+"""
+
+The main driving routines for this package are:
+
+* :func:`plot_contours <fgivenx.drivers.plot_contours>`
+* :func:`plot_lines <fgivenx.drivers.plot_lines>`
+* :func:`plot_dkl <fgivenx.drivers.plot_dkl>`
+* :func:`samples_from_getdist_chains <fgivenx.samples.samples_from_getdist_chains>`
+
+Example import and usage:
+
+>>> import numpy
+>>> from fgivenx import plot_contours, plot_lines, plot_dkl, samples_from_getdist_chains
+>>> 
+>>> file_root = '/my/getdist/file/root'
+>>> params = ['m', 'c']
+>>> samples = samples_from_getdist_chains(params, file_root)
+>>> x = numpy.linspace(-1, 1, 100)
+>>> 
+>>> def f(x, theta):
+>>>     m, c = params
+>>>     y = m * x + c
+>>>     return y
+>>> 
+>>> plot_contours(f, x, samples)
+"""
+
 from fgivenx.drivers import plot_contours, plot_lines, plot_dkl
 from fgivenx.samples import samples_from_getdist_chains

paper/paper.bib

@@ -110,13 +110,12 @@ @ARTICLE{Higson2018
 
 @article{zenodo,
     Author = {Handley, W},
-    Date-Modified = {2018-07-12 11:21:25 +0000},
-    doi = {10.5281/zenodo.1310715},
-    Month = {Jul},
+    doi = {10.5281/zenodo.1344097},
+    Month = {Aug},
     Publisher = {Zenodo},
-    Title = {fgivenx: v2.0},
+    Title = {fgivenx: v2.1.10},
     Year = {2018},
-    Bdsk-Url-1 = {http://dx.doi.org/10.5281/zenodo.1310715}
+    Bdsk-Url-1 = {http://dx.doi.org/10.5281/zenodo.1344097}
 }
 
 @unpublished{Higson2018b,

paper/paper.md

@@ -78,8 +78,8 @@ sensing [@Higson2018b].
 used in astronomy, but will be of use to scientists performing any Bayesian
 analysis which has predictive posteriors that are functions. The source code
 for ``fgivenx`` is available on
-[GitHub](https://github.com/williamjameshandley/fgivenx) and has been archived to
-Zenodo with the linked DOI: [@zenodo] 
+[GitHub](https://github.com/williamjameshandley/fgivenx) and has been archived
+as ``v2.1.11`` to Zenodo with the linked DOI: [@zenodo] 
 
 # Acknowledgements