Py API docs (cyclus#226)

LGTM! thx @scopatz for putting this.
mbmcgarry · Jan 31, 2017 · 22635de · 22635de
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diff --git a/source/arche/tutorial/index.rst b/source/arche/tutorial/index.rst
@@ -29,15 +29,13 @@ This tutorial has the following steps:
     testing
     input_files
 
-.. ::
+Given enough time, the following extra topics may be covered:
 
-   Given enough time, the following extra topics may be covered:
-
-   .. toctree::
-       :maxdepth: 1
+.. toctree::
+    :maxdepth: 1
 
-       cyclist
-       dre
+    cyclist
+    dre
 
 .. note::
 

diff --git a/source/astatic/CVT-logo-250pix1.png b/source/astatic/CVT-logo-250pix1.png
diff --git a/source/basics/projects.rst b/source/basics/projects.rst
@@ -8,7 +8,7 @@ method developments purposes.
 Consortium for Verification Technology
 --------------------------------------
 
-.. figure:: http://cvt.engin.umich.edu/wp-content/uploads/sites/173/2014/10/CVT-logo-250pix1.png
+.. figure:: ../astatic/CVT-logo-250pix1.png
     :align: right
     :width: 100
 

diff --git a/source/cite/index.rst b/source/cite/index.rst
@@ -22,7 +22,7 @@ The following are presentations given about |cyclus|:
 
 * `Cyclus: Next Generation Fuel Cycle Simulator <http://dx.doi.org/10.6084/m9.figshare.1278926>`_, presented at the Fuel Cycle Options Campaign meeting, 12/16/14, Las Vegas, NV
 * `Market-Based and System-Wide Fuel Cycle Optimization <http://figshare.com/articles/Market_Based_and_System_Wide_Fuel_Cycle_Optimization/1278937>`_, presented at the Fuel Cycle Options Campaign meeting, 12/16/14, Las Vegas, NV
-   
+
 
 
 |Cyclus| Meetings and Tutorials
@@ -35,7 +35,7 @@ The |Cyclus| community will occasionally hold meetings and tutorials, with docum
     :glob:
 
     meetings/*
-
+    tutorials/*
 
 
 

diff --git a/source/conf.py b/source/conf.py
@@ -44,10 +44,10 @@
 
 # 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.pngmath', 'sphinx.ext.autodoc', 
+extensions = ['sphinx.ext.imgmath', 'sphinx.ext.autodoc',
               'sphinx.ext.autosummary',
               'numpydoc',
-              'cyclusagent', 'cloud_sptheme.ext.table_styling', 
+              'cyclusagent', 'cloud_sptheme.ext.table_styling',
               'sphinxcontrib.bibtex']
 
 numpydoc_show_class_members = False
@@ -74,7 +74,8 @@
 # built documents.
 verout = ""
 try:
-    verout = subprocess.check_output('cyclus --version', shell=True).split()
+    verout = subprocess.check_output('cyclus --version', shell=True,
+                                     universal_newlines=True).split()
 except OSError:
     warnings.warn("WARNING: Continuing without cyclus - will not include "
                   "agents in output", RuntimeWarning)
@@ -97,7 +98,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns = ['python/blank.rst']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
@@ -291,11 +292,11 @@
 #texinfo_show_urls = 'footnote'
 
 rst_epilog = """
-.. |cyclus| raw:: html 
+.. |cyclus| raw:: html
 
        <span style="font-variant:small-caps;">Cyclus</span>
 
-.. |Cyclus| raw:: html 
+.. |Cyclus| raw:: html
 
        <span style="font-variant:small-caps;">Cyclus</span>
 """
diff --git a/source/index.rst b/source/index.rst
@@ -24,7 +24,7 @@ simulation <fuel cycle simulator>` while providing a low barrier to entry for
 new users and agent developers. |Cyclus| engages with potential module
 developers and encourages them to join a vibrant community in an
 :doc:`expanding ecosystem <basics/ecosystem>`.  Users and developers are
-always welcome and encouraged to use or contribute to the |cyclus| project. 
+always welcome and encouraged to use or contribute to the |cyclus| project.
 
 The |Cyclus| project repository is located at http://github.com/cyclus/cyclus
 
@@ -39,16 +39,22 @@ News
 
 **December 13, 2016:** :doc:`Cyclus v1.5.0 is released <previous/v1.5>`
 
-**July 6-8, 2016:** :doc:`Technical workshop on Dynamic Fuel Cycle>` in Paris, France
+**July 6-8, 2016:** Technical workshop on Dynamic Fuel Cycle in Paris, France
 
 **August 13, 2015:** :doc:`Cyclus included in FY2016 workscopes for the NEUP program <news/fy16neup>`
 
 **July 21-24, 2015:** Joint workshop with CLASS_ project held in Madison, WI
 
-**June 10, 2015:** First Cyclus :doc:`user tutorial <user/tutorial/index>` and :doc:`developer tutorial <arche/tutorial/index>` are held at the 2015 ANS Annual Meeting in San Antonio, TX 
+**June 10, 2015:** First Cyclus :doc:`user tutorial <user/tutorial/index>` and :doc:`developer tutorial <arche/tutorial/index>` are held at the 2015 ANS Annual Meeting in San Antonio, TX
 
 **June 7, 2015:** :doc:`Cyclus v1.3.1 is released <previous/v1.3>`
 
+.. toctree::
+    :maxdepth: 1
+
+    news/fy16neup
+
+
 Learn More
 ----------
 
@@ -59,6 +65,7 @@ Learn More
     user/index
     arche/index
     kernel/index
+    python/index
     cep/cep0
     previous/index
     cite/index
@@ -98,7 +105,7 @@ this page.  It contains all submitted jobs - their status, output, and database
     <div id="dashboard"></div>
     <br>
 
-    <script> 
+    <script>
         var server = "http://cycrun.fuelcycle.org"
 
         function submitJob() {
@@ -181,7 +188,7 @@ Support for this research has included funding received from:
 
     .. image :: astatic/neup_logo_large.png
         :height: 100 px
- 
+
     .. image :: astatic/AnlLogo.png
         :height: 100 px
 

diff --git a/source/python/blank.rst b/source/python/blank.rst
@@ -0,0 +1,11 @@
+.. _cyclus_pyapi_mod:
+
+********************************************************************************
+ (``cyclus.mod``)
+********************************************************************************
+
+.. automodule:: cyclus.mod
+    :members:
+    :undoc-members:
+    :inherited-members:
+
diff --git a/source/python/events.rst b/source/python/events.rst
@@ -0,0 +1,11 @@
+.. _cyclus_pyapi_events:
+
+********************************************************************************
+Event Loop (``cyclus.events``)
+********************************************************************************
+
+.. automodule:: cyclus.events
+    :members:
+    :undoc-members:
+    :inherited-members:
+
diff --git a/source/python/index.rst b/source/python/index.rst
@@ -0,0 +1,35 @@
+.. summary Python Documentation for |Cyclus|
+
+|Cyclus| Python Interface
+=========================
+This covers the Python bindings for |Cyclus| and related utilities.
+
+Low-level Python Wrappers
+-------------------------
+
+.. toctree::
+    :maxdepth: 1
+
+    typesystem
+    lib
+    main
+
+
+Python & C++ Interop Modules
+----------------------------
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    events
+
+
+Helpers & Utilities
+----------------------------
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    jsoncpp
diff --git a/source/python/jsoncpp.rst b/source/python/jsoncpp.rst
@@ -0,0 +1,11 @@
+.. _cyclus_pyapi_jsoncpp:
+
+********************************************************************************
+JSON C++ (``cyclus.jsoncpp``)
+********************************************************************************
+
+.. automodule:: cyclus.jsoncpp
+    :members:
+    :undoc-members:
+    :inherited-members:
+
diff --git a/source/python/lib.rst b/source/python/lib.rst
@@ -0,0 +1,11 @@
+.. _cyclus_pyapi_lib:
+
+********************************************************************************
+Cyclus Library Bindings (``cyclus.lib``)
+********************************************************************************
+
+.. automodule:: cyclus.lib
+    :members:
+    :undoc-members:
+    :inherited-members:
+
diff --git a/source/python/main.rst b/source/python/main.rst
@@ -0,0 +1,11 @@
+.. _cyclus_pyapi_main:
+
+********************************************************************************
+Main Command Lin Interface (``cyclus.main``)
+********************************************************************************
+
+.. automodule:: cyclus.main
+    :members:
+    :undoc-members:
+    :inherited-members:
+
diff --git a/source/python/typesystem.rst b/source/python/typesystem.rst
@@ -0,0 +1,11 @@
+.. _cyclus_pyapi_typesystem:
+
+********************************************************************************
+Cyclus Type System (``cyclus.typesystem``)
+********************************************************************************
+
+.. automodule:: cyclus.typesystem
+    :members:
+    :undoc-members:
+    :inherited-members:
+
diff --git a/source/user/cymetric/api/cyclus.rst b/source/user/cymetric/api/cyclus.rst
diff --git a/source/user/cymetric/api/index.rst b/source/user/cymetric/api/index.rst
@@ -1,7 +1,7 @@
 Cymetric API
 ============
 The following modules make up the cymetric package.  Note that most of the
-important stuff you can get directly from ``cymetric`` without needing to import 
+important stuff you can get directly from ``cymetric`` without needing to import
 the module.  For example, the following two imports are the same:
 
 .. code-block:: python
@@ -15,7 +15,6 @@ the module.  For example, the following two imports are the same:
 .. toctree::
     :maxdepth: 1
 
-    typesystem
     schemas
     metrics
     root_metrics
@@ -27,6 +26,5 @@ the module.  For example, the following two imports are the same:
 .. toctree::
     :maxdepth: 1
 
-    cyclus
     main
     tools
diff --git a/source/user/cymetric/api/typesystem.rst b/source/user/cymetric/api/typesystem.rst