Merge pull request #379 from rmcgibbo/2.8.1-bugfix

2.8.1 bugfix

Author: rmcgibbo

MANIFEST.in

@@ -5,6 +5,6 @@ include RevisionHistory.txt
 graft src
 graft reference
 graft tests
-graft TUTORIAL/xtc
+graft Tutorial
 graft Docs
 graft Extras

scripts/Interactive-SCRE.py scripts/InteractiveSCRE.pyscripts/Interactive-SCRE.py renamed to scripts/InteractiveSCRE.py

@@ -8,7 +8,6 @@
 from msmbuilder import MSMLib, SCRE, arglib
 import numpy as np
 import string
-import matplotlib
 import logging
 logger = logging.getLogger('msmbuilder.scripts.Interactive-SCRE')
 
@@ -89,6 +88,7 @@ def scre_iteration(assignments,K0,lagtime_list,M,X,populations):
 run = interactive_scre
 
 if __name__ == "__main__":
+    import matplotlib
     args = parser.parse_args()
 
     try:

scripts/PlotImpliedTimescales.py

@@ -17,7 +17,6 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
-from pylab import *
 from numpy import loadtxt
 import sys
 from msmbuilder import arglib
@@ -37,6 +36,7 @@
                     default='Relaxation Timescale versus Lagtime')
 
 if __name__ == '__main__':
+    from pylab import *
     args = parser.parse_args()
     input = np.loadtxt(args.input)
 

scripts/__init__.py

@@ -32,11 +32,11 @@
  'ConvertDataToHDF',
  'CreateAtomIndices',
  'FindPaths',
- 'Interactive-SCRE',
+ 'InteractiveSCRE',
  'PCCA',
  'PlotImpliedTimescales',
  'RebuildProject',
  'SampleTrajectory',
  'SaveStructures',
  'TrimAssignments',
- 'tICA_train']
+ 'tICA_train']

setup.py

@@ -20,8 +20,8 @@
     from distutils.core import setup
 
 #########################################
-VERSION = "2.8"
-ISRELEASED = False
+VERSION = "2.8.1"
+ISRELEASED = True
 __author__ = "MSMBuilder Team"
 __version__ = VERSION
 ########################################
@@ -83,7 +83,7 @@ class VersionError(Exception):
     'package_dir': {'msmbuilder': 'src/python', 'msmbuilder.scripts': 'scripts',
                     'msmbuilder.reference': 'reference'},
     'package_data': {'msmbuilder.reference': [os.path.relpath(os.path.join(a[0], b), 'reference') for a in os.walk('reference') for b in a[2]]},
-    'scripts': ['scripts/msmb'] + [e for e in glob('scripts/*') if not e.endswith('__.py')]
+    'scripts': ['scripts/msmb'] + [e for e in glob('scripts/*') if (not e.endswith('__.py')) or e.endswith('.pyc')]
 }
 
 if 'setuptools' in sys.modules:

src/python/SCRE.py

@@ -3,7 +3,6 @@
 import scipy.linalg
 import scipy.optimize
 import scipy.stats
-import matplotlib
 
 
 def GetFormat():
@@ -240,6 +239,7 @@ def PlotRates(KList, LagTimeList, counts_list, Tau=1):
         The time unit associated with spacings between lagtimes.
         
     """
+    import matplotlib
     KList = np.array(KList)
     NumStates = KList.shape[-1]
     TauList = Tau / KList