Merge pull request prody#1942 from jamesmkrieger/change_website

update website throughout prody

Author: jamesmkrieger

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-This is a first draft, which is based on the ProDy website page http://prody.csb.pitt.edu/manual/devel/develop.html. Please see that page for updates.
+This is a first draft, which is based on the ProDy website page http://www.bahargroup.org/prody/manual/devel/develop.html. Please see that page for updates.
 
 
 Install Git and a GUI

PKG-INFO

@@ -32,23 +32,23 @@ Description: .. image:: https://secure.travis-ci.org/prody/ProDy.png?branch=mast
         You can run ProDy on all major platforms.  For download and installation
         instructions see:
 
-        * http://prody.csb.pitt.edu/downloads
+        * http://www.bahargroup.org/prody/downloads
 
 
         DOCUMENTATION
         -------------
 
-        * Homepage: http://prody.csb.pitt.edu/
+        * Homepage: http://www.bahargroup.org/prody/
 
-        * Tutorials: http://prody.csb.pitt.edu/tutorials
+        * Tutorials: http://www.bahargroup.org/prody/tutorials
 
-        * Reference: http://prody.csb.pitt.edu/manual
+        * Reference: http://www.bahargroup.org/prody/manual
 
-        * Applications: http://prody.csb.pitt.edu/manual/apps
+        * Applications: http://www.bahargroup.org/prody/manual/apps
 
-        * NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
+        * NMWiz GUI: http://www.bahargroup.org/prody/nmwiz
 
-        * Changes: http://prody.csb.pitt.edu/manual/release
+        * Changes: http://www.bahargroup.org/prody/manual/release
 
 
         SOURCE CODE

docs/apps/prody/index.rst

@@ -40,4 +40,4 @@ the output files are prefixed with :file:`p38_anm`::
 
 The output file :file:`p38_anm.nmd` can be visualized using `NMWiz`_.
 
-.. _NMWiz: http://prody.csb.pitt.edu/nmwiz/
+.. _NMWiz: http://www.bahargroup.org/prody/nmwiz/

docs/conf.py

@@ -158,13 +158,13 @@
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
     'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
     'matplotlib': ('http://matplotlib.sourceforge.net/', None),
-    'prodywebsite': ('http://prody.csb.pitt.edu/', None),
+    'prodywebsite': ('http://www.bahargroup.org/prody/', None),
 }
 
 rst_epilog = u"""
 
-.. _ProDy: http://prody.csb.pitt.edu
-.. _Tutorials: http://prody.csb.pitt.edu/tutorials
+.. _ProDy: http://www.bahargroup.org/prody
+.. _Tutorials: http://www.bahargroup.org/prody/tutorials
 .. _NMWiz: http://csb.pitt.edu/NMWiz
 .. _VMD: http://www.ks.uiuc.edu/Research/vmd
 .. _PDB: http://www.pdb.org

docs/index.rst

@@ -11,7 +11,7 @@ ProDy Manual
 .. only:: rtd and html
 
     This is a partial copy of ProDy documentation.  Please visit
-    `ProDy Homepage <http://prody.csb.pitt.edu>`_ for complete
+    `ProDy Homepage <http://www.bahargroup.org/prody>`_ for complete
     documentation with tutorials.
 
 

prody/ensemble/functions.py

@@ -411,7 +411,7 @@ def buildPDBEnsemble(atomics, ref=None, title='Unknown', labels=None, atommaps=N
 
     if 'mapping_func' in kwargs:
         raise DeprecationWarning('mapping_func is deprecated. Please see release notes for '
-                                 'more details: http://prody.csb.pitt.edu/manual/release/v1.11_series.html')
+                                 'more details: http://www.bahargroup.org/prody/manual/release/v1.11_series.html')
     start = time.time()
 
     if not isListLike(atomics):