Update headers, fix style for some py files

[alexxy/gromacs.git] / src / python / runner / pipeline.py

diff --git a/src/python/runner/pipeline.py b/src/python/runner/pipeline.py
index f0dbb796620fbe3bb15abc83447ee6669fd2720b..48106cbb3fe904052a6d01fcebf5562b5acd1ce2 100644 (file)
--- a/src/python/runner/pipeline.py
+++ b/src/python/runner/pipeline.py
@@ -1,13 +1,49 @@
-
-from gromacs import Options, TrajectoryAnalysis
-import sys, shlex
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+import sys
+import shlex
+from gromacs import Options
+from gromacs import TrajectoryAnalysis
 
 class GromacsPipeline(TrajectoryAnalysis.TrajectoryAnalysisModule):
 
     def __init__(self,
         name="PythonPipeline",
         description="Pipeline of modules created with Python",
-        modules=[]
+        modules=[],
+        keep_datasets=False,
     ):
         super(GromacsPipeline, self).__init__(name, description)
 
@@ -26,11 +62,15 @@ class GromacsPipeline(TrajectoryAnalysis.TrajectoryAnalysisModule):
 
             options_list = [name] + shlex.split(options)
 
+            if keep_datasets:
+                for i in range(module.datasetCount()):
+                    module.datasetFromIndex(i).requestStorage(-1)
+
             self.modules.append(module)
             self.options.append(options_list)
 
     def initOptions(self, options, settings):
-        options.setDescription(self.description())
+        settings.setHelpText(self.description())
 
     def getBatch(self):
         return self.modules
@@ -56,6 +96,8 @@ class GromacsPipeline(TrajectoryAnalysis.TrajectoryAnalysisModule):
 
         TrajectoryAnalysis.runAsMain(self, argv)
 
-def runPipeline(name="PythonPipeline", description="Pipeline of modules created with Python", modules=[], argv=None):
-    pipeline = GromacsPipeline(name, description, modules)
+def runPipeline(argv=None, *args, **kwargs):
+    pipeline = GromacsPipeline(*args, **kwargs)
     pipeline.run(argv)
+
+    return pipeline