Fixed installation bugs and updated relevant documentation.

.gitignore

@@ -1,3 +1,5 @@
+.DS_Store
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -26,7 +28,6 @@ coverage.xml
 *,cover
 .hypothesis/
 
-
 # Distribution / packaging
 .Python
 env/

docs/Makefile

@@ -53,7 +53,12 @@ help:
 
 .PHONY: clean
 clean:
-	rm -rf $(BUILDDIR)/*
+	rm -rf $(BUILDDIR)/doctrees
+	rm -rf $(BUILDDIR)/html/*.html
+	rm -rf $(BUILDDIR)/html/*.js
+	rm -rf $(BUILDDIR)/html/*.html
+	rm -rf $(BUILDDIR)/html/_sources
+	rm -rf $(BUILDDIR)/html/_static
 
 .PHONY: html
 html:

docs/source/distill.utils.rst

@@ -1,23 +1,23 @@
-Utilities Library
------------------
+Query Builder
+-------------
 
-.. automodule:: distill.utils
+.. automodule:: distill.utils.query_builder
     :members:
     :undoc-members:
     :show-inheritance:
 
 Exception Handling
 ------------------
 
-.. automodule:: distill.exceptions
-	:members:
-   :undoc-members:
+.. automodule:: distill.utils.exceptions
+    :members:
+    :undoc-members:
     :show-inheritance:
 
 Validation Library
 ------------------
 
-.. automodule:: distill.validation
+.. automodule:: distill.utils.validation
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/installation.rst

@@ -3,8 +3,8 @@
 Installation Guide
 ==================
 
-Installing Distill in an Development Environment
-------------------------------------------------
+Installing Distill
+------------------
 
 The first step is to install Distill. First, checkout the latest version of Distill.
 
@@ -24,7 +24,7 @@ or
 
     $ pip install distill
 
-Advanced users can install Distill in a virtualenv if they wish. Instructions to setup an virtual environment will be explained below.
+Users are strongly recommended to install Distill in a virtualenv. Instructions to setup an virtual environment will be explained below.
 
 .. note ::
 
@@ -33,23 +33,50 @@ Advanced users can install Distill in a virtualenv if they wish. Instructions to
 Installing Distill in an Virtual Environment
 --------------------------------------------
 
-	TODO
+virtualenv is a tool to create isolated Python environments. virtualenv creates a folder which contains all the necessary executables to use the packages that the Distill project would need. 
 
-Development and Testing
------------------------
+Install virtualenv via pip:
+
+::
+
+	$ sudo pip install virtualenv
+
+Start by changing directory into the root of Distill's project directory, and then use the virtualenv command-line tool to create a new environment:
+
+::
+
+	$ mkdir env 
+	$ virtualenv env
+
+Activate environment:
+
+::
+
+	$ source env/bin/activate
+
+Install Distill requirements:
+
+::
+
+	$ env/bin/pip -r requirements.txt
 
 To build the source code and run all unit tests.
 
 ::
 
-    $ python setup.py develop test
+    $ env/bin/python setup.py develop test
 
-To start up a local web server, running on localhost:8090.
+Launch local Distill server, running on localhost:8090:
 
 ::
+	
+	$ env/bin/dev 
+
+Deactivate environment
 
-    $ dev
+:: 	
 
+	$ deactivate
 
 Deployment
 ----------
@@ -75,7 +102,7 @@ Download the project from the GitHub repository and copy the application to the
 
 	$ git clone https://github.com/draperlaboratory/distill.git /home/public_html
 
-Install Distill's requirements.
+Install Distill's requirements either globally or in a virutal environment:
 
 ::
 

requirements.txt

@@ -5,3 +5,5 @@ numpy>=1.10.0
 scipy>=0.17.0
 sphinx>=1.4.0
 pandas>=0.18.1
+pytest>=2.9.0
+sphinx_rtd_theme>=0.1.9

setup.py

@@ -1,14 +1,18 @@
-'''
-Distill: An analytical framework for User-ALE <https://github.com/draperlaboratory/user-ale>.
-
-Note that "python setup.py test" invokes pytest on the package. With appropriately
-configured setup.cfg, this will check both xxx_test modules and docstrings.
-
-You can install Distill with "python setup.py install"
-
-Copyright 2016, The Charles Stark Draper Laboratory, Inc.
-Licensed under Apache Software License
-'''
+# -*- coding: utf-8 -*-
+#
+# Copyright 2016 The Charles Stark Draper Laboratory, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 from __future__ import absolute_import
 from setuptools import setup, find_packages
@@ -18,9 +22,6 @@
 if sys.version_info[:2] < (2, 7):
     m = "Python 2.7 or later is required for Distill (%d.%d detected)."
     raise ImportError (m % sys.version_info[:2])
-del sys
-
-#here = os.path.abspath(os.path.dirname (__file__) )
 
 if sys.argv[-1] == 'setup.py':
     print ("To install, run 'python setup.py install'")
@@ -54,7 +55,7 @@ def run_tests (self):
     license = "Apache Software License",
     author = "Michelle Beard",
     author_email = "mbeard@draper.com",
-    description = "An analytical framework for User-ALE.",
+    description = "An analytical framework for UserALE.",
     long_description = __doc__,
     classifiers = [
       'Development Status :: 4 - Beta',
@@ -67,11 +68,11 @@ def run_tests (self):
       'Operating System :: OS Independent', 
       'Private :: Do Not Upload"'
     ],
-    keywords = "analytics graph stout user-ale instrumentation", # Separate with spaces
+    keywords = "stout userale tap", # Separate with spaces
     packages = find_packages (exclude=['examples', 'tests']),
     include_package_data = True,
     zip_safe = False,
-    tests_require = ['pytest'],
+    tests_require = ['pytest>=2.9.0'],
     cmdclass = {'test': PyTest},
     install_requires = ['Flask==0.10.1', 
                         'networkx==1.11',