Added autodocs, updated theme.

source/api/index.rst

@@ -0,0 +1,9 @@
+###
+API
+###
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules

source/api/modules.rst

@@ -0,0 +1,7 @@
+thot
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   thot

source/api/thot.classes.rst

@@ -0,0 +1,78 @@
+thot.classes package
+====================
+
+Submodules
+----------
+
+thot.classes.asset module
+-------------------------
+
+.. automodule:: thot.classes.asset
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.base\_object module
+--------------------------------
+
+.. automodule:: thot.classes.base_object
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.container module
+-----------------------------
+
+.. automodule:: thot.classes.container
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.metadata module
+----------------------------
+
+.. automodule:: thot.classes.metadata
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.note module
+------------------------
+
+.. automodule:: thot.classes.note
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.role module
+------------------------
+
+.. automodule:: thot.classes.role
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.script module
+--------------------------
+
+.. automodule:: thot.classes.script
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.classes.thot\_interface module
+-----------------------------------
+
+.. automodule:: thot.classes.thot_interface
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: thot.classes
+    :members:
+    :undoc-members:
+    :show-inheritance:

source/api/thot.db.rst

@@ -0,0 +1,38 @@
+thot.db package
+===============
+
+Submodules
+----------
+
+thot.db.database\_interface module
+----------------------------------
+
+.. automodule:: thot.db.database_interface
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.db.local module
+--------------------
+
+.. automodule:: thot.db.local
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.db.mongo module
+--------------------
+
+.. automodule:: thot.db.mongo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: thot.db
+    :members:
+    :undoc-members:
+    :show-inheritance:

source/api/thot.rst

@@ -0,0 +1,46 @@
+thot package
+============
+
+Subpackages
+-----------
+
+.. toctree::
+
+    thot.classes
+    thot.db
+
+Submodules
+----------
+
+thot.runner module
+------------------
+
+.. automodule:: thot.runner
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.thot module
+----------------
+
+.. automodule:: thot.thot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+thot.utilities module
+---------------------
+
+.. automodule:: thot.utilities
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: thot
+    :members:
+    :undoc-members:
+    :show-inheritance:

source/conf.py

@@ -11,10 +11,10 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+
+import os
+import sys
+sys.path.insert( 0, os.path.abspath( '../python/' ) ) 
 
 
 # -- Project information -----------------------------------------------------
@@ -45,7 +45,7 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-# templates_path = []
+templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -76,8 +76,9 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = 'alabaster'
+
+# html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # 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
@@ -88,7 +89,7 @@
 # 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 = []
+html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

source/get_started.rst

@@ -191,9 +191,9 @@ There are only two changes you need to make to convert a local analysis script i
 2. ``thot = LocalProject()`` |rarr| ``thot = ThotProject()`` 
 
 
-********
-Analysis
-********
+***************
+Writing Scripts
+***************
 
 Thot is founded on the idea that the same analysis needs to be run on different data sets. Often this is done manually, taking additional time and effort, and is prone to mistakes. By separating the analysis process from the data, Thot allows your data to be automatically analyzed.
 

source/index.rst

@@ -16,7 +16,7 @@ Data management and analysis software.
    local_projects
    hosted_projects
    examples
-   api
+   api/index
 
 
 Indices and tables

source/overview.rst

@@ -20,12 +20,12 @@ Containers are the organizational building blocks of your project. They allow yo
 Assets
 ======
 
-An Asset is anything that is consumed or created in your analysis. This includes raw data, calculated data, and images. Each Asset can have descriptors and metadata attached to it as well.
+An Asset is anything that is consumed or created in your analysis. This includes raw data, calculated data, and images. Each Asset can have descriptors and metadata attached to it.
 
 Scripts
 =======
 
-A Script is a multi-input, multi-output function where the inputs and outputs are Assets. The input to a script is *consumed* and the output is *produced*. The produced Assets can then be consumed by other Scripts in the future.
+A Script is a multi-input, multi-output function whose inputs and outputs are Assets. The input to a script is *consumed* and the output is *produced*. The produced Assets can then be consumed by other Scripts in the future.
 
 Descriptors
 -----------
@@ -56,4 +56,4 @@ Thot utilizes a tree structure to organize data. Properties of children are inhe
 Analysis
 ********
 
-Thot is based on the idea that data and analysis should be separated and data should never be modified. You can think of a Thot analysis script as a machine reads data manipulates them and creates new pieces of data.
+Thot is based on the idea that data and analysis should be separated and data should never be modified. You can think of a Thot Script as a machine that reads data, manipulates them, and creates new data.