Populate API docs with sphinx-apidoc

sphinx-api doc searches requested paths to modules and creates an autodoc entry
for each module it finds. In this case, we autogenerated an `augur.rst` file and
reference that file's table of contents from a static API.rst file. The augur
API file was generated with the command `sphinx-apidoc -T -f -o docs augur` from
the top-level augur directory.

docs/APIdoc.rst

@@ -1,40 +1,7 @@
-.. augur documentation master file, created by
-   sphinx-quickstart on Tue Apr 23 21:32:18 2019.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+API
+===
 
-API documentation
-=================
+.. toctree::
+   :maxdepth: 4
 
-
-augur.tree
-----------
-.. automodule:: augur.tree
-	:members:
-
-
-augur.refine
-------------
-.. automodule:: augur.refine
-	:members:
-
-
-augur.titer_models
-------------------
-.. autoclass:: augur.titer_model.TiterCollection
-	:members:
-
-.. autoclass:: augur.titer_model.TiterModel
-	:members:
-
-.. autoclass:: augur.titer_model.TreeModel
-	:members:
-
-.. autoclass:: augur.titer_model.SubstitutionModel
-	:members:
-
-
-augur.traits
-------------
-.. automodule:: augur.refine
-	:members:
+   augur

docs/augur.rst

@@ -0,0 +1,198 @@
+augur package
+=============
+
+Submodules
+----------
+
+augur.align module
+------------------
+
+.. automodule:: augur.align
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.ancestral module
+----------------------
+
+.. automodule:: augur.ancestral
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.clades module
+-------------------
+
+.. automodule:: augur.clades
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.distance module
+---------------------
+
+.. automodule:: augur.distance
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.export module
+-------------------
+
+.. automodule:: augur.export
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.filenames module
+----------------------
+
+.. automodule:: augur.filenames
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.filter module
+-------------------
+
+.. automodule:: augur.filter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.frequencies module
+------------------------
+
+.. automodule:: augur.frequencies
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.frequency\_estimators module
+----------------------------------
+
+.. automodule:: augur.frequency_estimators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.lbi module
+----------------
+
+.. automodule:: augur.lbi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.mask module
+-----------------
+
+.. automodule:: augur.mask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.parse module
+------------------
+
+.. automodule:: augur.parse
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.reconstruct\_sequences module
+-----------------------------------
+
+.. automodule:: augur.reconstruct_sequences
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.refine module
+-------------------
+
+.. automodule:: augur.refine
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.sequence\_traits module
+-----------------------------
+
+.. automodule:: augur.sequence_traits
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.titer\_model module
+-------------------------
+
+.. automodule:: augur.titer_model
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.titers module
+-------------------
+
+.. automodule:: augur.titers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.traits module
+-------------------
+
+.. automodule:: augur.traits
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.translate module
+----------------------
+
+.. automodule:: augur.translate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.tree module
+-----------------
+
+.. automodule:: augur.tree
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.utils module
+------------------
+
+.. automodule:: augur.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.validate module
+---------------------
+
+.. automodule:: augur.validate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+augur.version module
+--------------------
+
+.. automodule:: augur.version
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: augur
+    :members:
+    :undoc-members:
+    :show-inheritance: