Merge pull request #98 from ColCarroll/update_docs

Update docs

.travis.yml

@@ -20,7 +20,7 @@ install:
 
   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy mkl scipy pandas matplotlib pytest pylint sphinx numpydoc ipython
   - source activate test-environment
-  - pip install -r requirements.txt
+  - pip install .
   - pip install -r requirements-dev.txt
   - pip install coveralls
 
@@ -33,7 +33,7 @@ before_script:
 script:
   - pylint arviz/
   - pytest -xv arviz/tests/ --cov=arviz/
-  - travis-sphinx build -n
+  - travis-sphinx build --nowarn --source=doc
 
 after_success:
   - travis-sphinx deploy

arviz/stats/stats.py

@@ -194,20 +194,20 @@ def gradient(weights):
 
     if np.any(weights):
         min_ic_i_val = ics[ic_i].iloc[0]
-        for i in ics.index:
-            res = ics.loc[i]
+        for idx, val in enumerate(ics.index):
+            res = ics.loc[val]
             diff = res[ic_i] - min_ic_i_val
             d_ic = np.sum(diff)
             d_std_err = np.sqrt(len(diff) * np.var(diff))
-            std_err = ses.loc[i]
-            weight = weights[i]
-            df_comp.at[i] = (round(res[ic], round_to),
-                             round(res[p_ic], round_to),
-                             round(d_ic, round_to),
-                             round(weight, round_to),
-                             round(std_err, round_to),
-                             round(d_std_err, round_to),
-                             res['warning'])
+            std_err = ses.loc[val]
+            weight = weights[idx]
+            df_comp.at[val] = (round(res[ic], round_to),
+                               round(res[p_ic], round_to),
+                               round(d_ic, round_to),
+                               round(weight, round_to),
+                               round(std_err, round_to),
+                               round(d_std_err, round_to),
+                               res['warning'])
 
     return df_comp.sort_values(by=ic)
 
@@ -220,13 +220,13 @@ def _ic_matrix(ics, ic_i):
     rows = len(ics[ic_i].iloc[0])
     ic_i_val = np.zeros((rows, cols))
 
-    for i in ics.index:
-        ic = ics.loc[i][ic_i]
+    for idx, val in enumerate(ics.index):
+        ic = ics.loc[val][ic_i]
         if len(ic) != rows:
             raise ValueError('The number of observations should be the same '
                              'across all models')
         else:
-            ic_i_val[:, i] = ic
+            ic_i_val[:, idx] = ic
 
     return rows, cols, ic_i_val
 

doc/.gitignore

@@ -0,0 +1,4 @@
+_build
+example_thumbs/
+examples/
+generated/

doc/_static/custom.css

@@ -0,0 +1,11 @@
+dt:target {
+  background-color: #E0FFFF;
+}
+
+a {
+  color: #12698A;
+}
+
+.navbar-brand img {
+  height: 150%;
+}

doc/api.rst

@@ -0,0 +1,57 @@
+.. _api:
+
+.. currentmodule:: arviz
+
+API Reference
+=============
+
+.. _plot_api:
+
+Plots
+-----
+
+.. autosummary::
+    :toctree: generated/
+
+    autocorrplot
+    compareplot
+    densityplot
+    energyplot
+    forestplot
+    kdeplot
+    parallelplot
+    posteriorplot
+    traceplot
+    pairplot
+    jointplot
+    khatplot
+    ppcplot
+
+.. _stats_api:
+
+Stats
+-----
+
+.. autosummary::
+    :toctree: generated/
+
+    bfmi
+    compare
+    hpd
+    loo
+    r2_score
+    summary
+    waic
+    psislw
+
+.. _diagnostics_api:
+
+Diagnostics
+-----------
+
+.. autosummary::
+    :toctree: generated/
+
+    effective_n
+    gelman_rubin
+    geweke

doc/source/conf.py → doc/conf.py

@@ -19,7 +19,7 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath(os.path.join('..', '..')))
+import sphinx_bootstrap_theme
 
 
 # -- General configuration ------------------------------------------------
@@ -31,19 +31,27 @@
 # 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',
+sys.path.insert(0, os.path.abspath('sphinxext'))
+extensions = [
+    'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
+    'sphinx.ext.coverage',
     'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
+    'sphinx.ext.autosummary',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
-    'sphinx.ext.napoleon',
     'matplotlib.sphinxext.only_directives',
     'matplotlib.sphinxext.plot_directive',
     'numpydoc',
     'nbsphinx',
-    'IPython.sphinxext.ipython_console_highlighting']
+    'IPython.sphinxext.ipython_console_highlighting',
+    'gallery_generator',
+]
 
+# Generate API documentation when building
+autosummary_generate = True
+numpydoc_show_class_members = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -95,36 +103,37 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'bootstrap'
 
 # 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 = {'logo_only': True}
+html_theme_options = {
+    'source_link_position': 'footer',
+    'navbar_title': ' ',
+    'globaltoc_depth': 0,
+    'bootswatch_theme': 'paper',
+    'navbar_pagenav': False,
+    'navbar_sidebarrel': False,
+    'navbar_links': [
+        ('Gallery', 'examples/index'),
+        ('Quickstart', 'notebooks/Introduction'),
+        ('API', 'api'),
+    ],
+}
 
 
 
 # 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']
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+html_static_path = ['_static', 'example_thumbs']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
-#
-# This is required for the alabaster theme
-# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
-html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-        'donate.html',
-    ]
-}
-
+#html_sidebars = {}
 
 # -- Options for HTMLHelp output ------------------------------------------
 

doc/index.rst

@@ -0,0 +1,76 @@
+ArviZ: Exploratory analysis of Bayesian models
+==============================================
+|Build Status|
+
+.. raw:: html
+
+
+    <div style="clear: both"></div>
+    <div class="container-fluid">
+        <div class="row">
+            <div class="col-md-6">
+
+
+ArviZ includes functions for posterior analysis, sample diagnostics, model checking, and comparison.
+
+It is currently in heavy development.  The goal is to provide backend-agnostic tools
+for Bayesian inference in Python. Currently `PyMC3
+<http://docs.pymc.io/>`_ is best supported,
+though many functions will work if the samples are stored in a pandas dataframe, and active work is being
+done to support `PyStan
+<https://pystan.readthedocs.io/en/latest/>`_ as well.
+
+Contributions and issue reports are very welcome at `the github repository
+<https://github.com/arviz-devs/arviz>`_.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   installation
+   Example Gallery<examples>
+   Quickstart<notebooks/Introduction>
+   api
+   about
+
+
+.. raw:: html
+
+    </div>
+    <div class="col-md-6">
+        <div class="container-fluid hidden-xs hidden-sm">
+            <a href="examples/energyplot.html">
+            <div class="col-md-3 thumbnail">
+                <img src="_static/energyplot_thumb.png">
+            </div>
+            </a>
+            <a href="examples/traceplot.html">
+            <div class="col-md-3 thumbnail">
+                <img src="_static/traceplot_thumb.png">
+            </div>
+            </a>
+            <a href="examples/densityplot.html">
+            <div class="col-md-3 thumbnail">
+                <img src="_static/densityplot_thumb.png">
+            </div>
+            </a>
+            <a href="examples/compareplot.html">
+            <div class="col-md-3 thumbnail">
+                <img src="_static/compareplot_thumb.png">
+            </div>
+            </a>
+            <a href="examples/autocorrplot.html">
+            <div class="col-md-3 thumbnail">
+                <img src="_static/autocorrplot_thumb.png">
+            </div>
+            </a>
+        </div>
+    </div>
+
+    </div>
+    </div>
+    </div>
+
+
+.. |Build Status| image:: https://travis-ci.org/arviz-devs/arviz.png?branch=master
+   :target: https://travis-ci.org/arviz-devs/arviz