cleanup of docs, including API, using sphinx_rtd_theme

Author: jonathan-taylor

.gitignore

@@ -39,4 +39,5 @@ build
 */*pyc
 *.pdf
 *.csv
-docs/api/generated/*
+doc/source/api/generated/*
+docs/source/api/generated/*

doc/Makefile

@@ -70,6 +70,7 @@ htmlonly:
 api:
 	-mkdir -p source/api/generated
 	python ../tools/build_modref_templates.py
+	-mv source/api/generated/gen.rst source/api
 	@echo "Build API docs finished."
 
 html: api htmlonly

doc/license.rst

@@ -0,0 +1,30 @@
+Copyright (c) 2015, Selective Inference development team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above
+       copyright notice, this list of conditions and the following
+       disclaimer in the documentation and/or other materials provided
+       with the distribution.
+
+    * The names of any contributors to this software
+       may not be used to endorse or promote products derived
+       from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.