[ProDy/el6] Merge branch 'master' into el6

[Antonio Trande]

commit 0a938b8b2b932a0f2fe237e512ef0326ab4173d4
Author: sagitter <anto.trande at gmail.com>
Date:   Sun Jul 13 17:39:44 2014 +0200

    Merge branch 'master' into el6
    
    Conflicts:
    	.gitignore
    	ProDy.spec
    	sources

 .gitignore |    6 +++++
 ProDy.spec |   67 ++++++++++++++++++++++++++++++++++--------------------------
 sources    |    2 +-
 3 files changed, 45 insertions(+), 30 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index 788df8a..35fd414 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,8 @@
 /ProDy-1.4.6.tar.gz
 /ProDy-1.4.8.tar.gz
+<<<<<<< HEAD
+=======
+/ProDy-1.4.9.tar.gz
+/ProDy-1.4.10.tar.gz
+/ProDy-1.5.1.tar.gz
+>>>>>>> master
diff --git a/ProDy.spec b/ProDy.spec
index b1e9136..0a64f4e 100644
--- a/ProDy.spec
+++ b/ProDy.spec
@@ -1,7 +1,10 @@
-%if 0%{?fedora}
-%global __python %{__python2}
+%if 0%{?rhel} && 0%{?rhel} <= 6
+%{!?__python2: %global __python2 /usr/bin/python2}
+%{!?python2_sitelib: %global python2_sitelib %(%{__python2} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")}
+%{!?python2_sitearch: %global python2_sitearch %(%{__python2} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib(1))")}
 %endif
 
+
 ##  Filtering of private libraries 
 %global _privatelibs  ^%{python_sitearch}/prody/.*\\.so$
 %global __provides_exclude_from ^(%{_privatelibs})$
@@ -9,8 +12,8 @@
 
 Name: ProDy
 Summary: Application for protein structure, dynamics and sequence analysis
-Version: 1.4.8
-Release: 1%{?dist}
+Version: 1.5.1
+Release: 3%{?dist}
 License: GPLv3+
 Group: Applications/Engineering
 URL: http://www.csb.pitt.edu/ProDy
@@ -31,16 +34,14 @@ Requires: python-matplotlib
 #
 ### argparse is used to implement applications and provided for
 ## compatibility with Python 2.6.
-#%if 0%{?rhel}
-#Requires: python-argparse
-#Requires: pyparsing, python-biopython >= 1.62
-#Requires: ipython
-#%else
+%if 0%{?rhel}
+Requires: python-argparse
+Requires: pyparsing, python-biopython >= 1.62
+Requires: python-ipython
+%else
 Requires: pyparsing, python-biopython
 Requires: python-ipython
-#%endif
-
- 
+%endif
 
 %description
 ProDy is a free and open-source Python package for protein structure, dynamics,
@@ -55,35 +56,43 @@ visual analysis.
 %setup -q -n %{name}-%{version}
 
 ## Removing bundled files
-rm lib/prody/atomic/pyparsing*
-rm -rf lib/prody/KDTree
-rm lib/prody/proteins/pairwise2.py
-rm lib/prody/apps/argparse.py
-
+rm prody/atomic/pyparsing*
+rm -rf prody/KDTree
+rm prody/proteins/pairwise2.py prody/proteins/cpairwise2.c
+rm prody/apps/argparse.py
 
 %build
-%{__python} setup.py build
+%{__python2} setup.py build
 
 %install
-%{__python} setup.py install --skip-build --root $RPM_BUILD_ROOT 
-
-## Fix 'non-executable-script' warnings
-chmod a+x $RPM_BUILD_ROOT%{python_sitearch}/prody/tests/test_*/test_*.py
-chmod a+x $RPM_BUILD_ROOT%{python_sitearch}/prody/tests/__init__.py
-
-## Add Python shebang 
-sed -i -e '1i#!/usr/bin/python' $RPM_BUILD_ROOT%{python_sitearch}/prody/tests/test_apps/test_prody_examples.py
+%{__python2} setup.py install --skip-build --root $RPM_BUILD_ROOT 
 
 %files
 %doc *.rst PKG-INFO
 %{_bindir}/prody
 %{_bindir}/evol
-%{python_sitearch}/prody
-%{python_sitearch}/%{name}-%{version}-*.egg-info
+%{python2_sitearch}/prody
+%{python2_sitearch}/%{name}-%{version}-*.egg-info
 
 %changelog
+* Sat Jul 12 2014 Antonio Trande <sagitter at fedoraproject.org> 1.5.1-3
+- Some fixes based on Python guidelines 
+
+* Fri Jun 06 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.5.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
+
+* Fri Jan 03 2014 Antonio Trande <sagitter at fedoraproject.org> 1.5.1-1
+- Update to 1.5.1
+
+* Mon Nov 25 2013 Antonio Trande <sagitter at fedoraproject.org> 1.4.10-1
+- Update to 1.4.10
+
+* Sat Nov 16 2013 Antonio Trande <sagitter at fedoraproject.org> 1.4.9-1
+- Update to 1.4.9
+- Remove 'cpairwise2.c' file
+
 * Wed Nov 06 2013 Antonio Trande <sagitter at fedoraproject.org> 1.4.8-1
-- Re-defined required packages for EPEL (still unused)
+- Re-defined required packages for EPEL
 - Update to 1.4.8
 
 * Thu Oct 24 2013 Antonio Trande <sagitter at fedoraproject.org> 1.4.6-2
diff --git a/sources b/sources
index 27cbc62..b36dddf 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-26a6192dcc742ce0f7becd3b4f89faa8  ProDy-1.4.8.tar.gz
+30bfbc8566269d4c9eb5998ba9025728  ProDy-1.5.1.tar.gz