pretty up the docs.

SchiefLab · Feb 14, 2018 · 9d9352f · 9d9352f
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Showing 12 changed files with 27 additions and 25 deletions.
diff --git a/docs/apps_pilot_api/apps.pilot.jadolfbr.rst b/docs/apps_pilot_api/apps.pilot.jadolfbr.rst
@@ -1,5 +1,5 @@
-apps.pilot.jadolfbr Apps
-========================
+apps.pilot.jadolfbr
+===================
 
 .. automodule:: apps.pilot.jadolfbr
     :members:

diff --git a/docs/apps_pilot_api/apps.pilot.rst b/docs/apps_pilot_api/apps.pilot.rst
@@ -6,8 +6,7 @@ Pilot Apps
     :undoc-members:
     :show-inheritance:
 
-Apps
-----
-
 .. toctree::
+    :maxdepth: 2
+
     apps.pilot.jadolfbr
diff --git a/docs/apps_public_api/apps.public.antibody_benchmark_utils.rst b/docs/apps_public_api/apps.public.antibody_benchmark_utils.rst
@@ -1,5 +1,5 @@
-public.antibody\_benchmark\_utils Apps
-======================================
+public.antibody\_benchmark\_utils
+=================================
 
 .. automodule:: apps.public.antibody_benchmark_utils
     :members:

diff --git a/docs/apps_public_api/apps.public.antibody_utils.rst b/docs/apps_public_api/apps.public.antibody_utils.rst
@@ -1,5 +1,5 @@
-public.antibody\_utils Apps
-===========================
+public.antibody\_utils
+======================
 
 .. automodule:: apps.public.antibody_utils
     :members:

diff --git a/docs/apps_public_api/apps.public.general.rst b/docs/apps_public_api/apps.public.general.rst
@@ -1,5 +1,5 @@
-public.general Apps
-===================
+public.general
+==============
 
 .. automodule:: apps.public.general
     :members:

diff --git a/docs/apps_public_api/apps.public.pdb_utils.rst b/docs/apps_public_api/apps.public.pdb_utils.rst
@@ -1,5 +1,5 @@
-public.pdb\_utils Apps
-======================
+public.pdb\_utils
+=================
 
 .. automodule:: apps.public.pdb_utils
     :members:

diff --git a/docs/apps_public_api/apps.public.pyrosetta.rst b/docs/apps_public_api/apps.public.pyrosetta.rst
@@ -1,6 +1,5 @@
-public.pyrosetta Apps
-=====================
-
+public.pyrosetta
+================
 .. automodule:: apps.public.pyrosetta
     :members:
     :undoc-members:

diff --git a/docs/apps_public_api/apps.public.rosetta.rst b/docs/apps_public_api/apps.public.rosetta.rst
@@ -1,5 +1,5 @@
-public.rosetta Apps
-===================
+public.rosetta
+==============
 
 .. automodule:: apps.public.rosetta
     :members:

diff --git a/docs/apps_public_api/apps.public.rst b/docs/apps_public_api/apps.public.rst
@@ -6,9 +6,6 @@ Public Apps
     :undoc-members:
     :show-inheritance:
 
-Apps
-----
-
 .. toctree::
     :maxdepth: 2
 

diff --git a/docs/apps_public_api/modules.rst b/docs/apps_public_api/modules.rst
@@ -2,6 +2,12 @@ Public Apps
 ======
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 1
 
    apps.public
+   apps.public.antibody_benchmark_utils
+   apps.public.antibody_utils
+   apps.public.general
+   apps.public.pdb_utils
+   apps.public.pyrosetta
+   apps.public.rosetta
diff --git a/docs/index.rst b/docs/index.rst
@@ -8,9 +8,10 @@ Contents:
 
    readme
    installation
+   api/modules
    apps_public_api/apps.public
    apps_pilot_api/apps.pilot
-   api/modules
+
 
 Indices and tables
 ==================

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -32,7 +32,7 @@ You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone git://github.com/jadolfbr/jade
+    $ git clone git://github.com/SchiefLab/jade
 
 Or download the `tarball`_:
 
@@ -53,7 +53,7 @@ Don't forget to source your bashrc/bash_profile or whatever other shell profile
 Scripts
 =======
 
-All scripts and applications in jade/apps will be installed in your bin directory and available for use.
+All scripts and applications in jade/apps will be installed in your bin directory and available for use. 
 
 
 .. _Github repo: https://github.com/SchiefLab/Jade