From 7ab4bd219c53eae08dc4aad42736fdea31fa4063 Mon Sep 17 00:00:00 2001
From: "John Chodera (MSKCC)" <choderaj@mskcc.org>
Date: Sat, 31 Dec 2016 16:32:09 -0500
Subject: [PATCH] Fix some documentation issues

---
 docs/analysis.rst        |  5 ++++-
 docs/conf.py             | 24 +++++++++++++++++++-----
 docs/getting_started.rst | 11 +++++------
 3 files changed, 28 insertions(+), 12 deletions(-)

diff --git a/docs/analysis.rst b/docs/analysis.rst
index 7f9989d..4e8a2a5 100644
--- a/docs/analysis.rst
+++ b/docs/analysis.rst
@@ -2,6 +2,10 @@
 
 .. currentmodule:: assaytools
 
+.. note::
+   This section is under heavy construction!
+   For now, see the examples directory: https://github.com/choderalab/assaytools/tree/master/examples
+
 Analysis Functions
 ==================
 
@@ -11,4 +15,3 @@ Here's an example ::
 
     >>> import assaytools
     >>> dataset = assaytools.load('dataset.xml')
-
diff --git a/docs/conf.py b/docs/conf.py
index f7efcdb..4489eee 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -18,12 +18,26 @@
 #import assaytools
 #import assaytools.version
 
-# Use mock to make our code think that numpy and scipy are available, even though they might not be available on readthedocs
-import mock
+import sys
+try:
+    from unittest.mock import MagicMock
+except ImportError:
+    from mock import Mock as MagicMock
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return MagicMock()
 
-MOCK_MODULES = ['numpy', 'scipy', 'numpy.linalg', 'scipy.special', 'scipy.stats', 'pymc', 'pint']
-for mod_name in MOCK_MODULES:
-    sys.modules[mod_name] = mock.Mock()
+MOCK_MODULES = ['numpy', 'scipy', 'numpy.linalg', 'scipy.special', 'scipy.stats', 'pymc', 'pint', 'pandas']
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
+# Use mock to make our code think that numpy and scipy are available, even though they might not be available on readthedocs
+#import mock
+#
+#MOCK_MODULES = ['numpy', 'scipy', 'numpy.linalg', 'scipy.special', 'scipy.stats', 'pymc', 'pint']
+#for mod_name in MOCK_MODULES:
+#    sys.modules[mod_name] = mock.Mock()
 
 # 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
diff --git a/docs/getting_started.rst b/docs/getting_started.rst
index 0ae8861..3ee87cf 100644
--- a/docs/getting_started.rst
+++ b/docs/getting_started.rst
@@ -10,15 +10,11 @@ Install with conda
 ------------------
 .. _install-with-conda:
 
-To install `AssayTools` with `conda <conda.pydata.org>`_`, use the following commands:
+To install `AssayTools` and its dependencies with `conda <conda.pydata.org>`_`, use the following commands:
 
 ::
-   $ conda install -c omnia assaytools
 
-.. note::
-   ``conda`` will automatically all of the tricky dependencies from binary packages automatically!
-   This includes :mod:`pytables`, :mod:`numpy`, :mod:`scipy`, :mod:`pandas`, and :mod:`pymc`!
-   The easiest way to get ``conda`` is with the `Anaconda python distribution <https://store.continuum.io/cshop/anaconda/>`_, or its smaller version `Miniconda <http://conda.pydata.org/miniconda.html>`_.
+   $ conda install -c omnia assaytools
 
 Install from source
 -------------------
@@ -27,6 +23,7 @@ Install from source
 You can install the latest development version of ``AssayTools`` from github via ``pip``:
 
 ::
+
    $ pip install git+https://github.com/choderalab/assaytools.git
 
 Testing Your Installation
@@ -37,9 +34,11 @@ Running the tests is a great way to verify that everything is working.
 The test suite uses `nose <https://nose.readthedocs.org/en/latest/>`_, which you can install via ``conda``:
 
 ::
+
    $ conda install nose
 
 Then, to run the tests:
 
 ::
+
    $ nosetests -vv assaytools