Merge branch 'master' into pygromacs

Change-Id: I3cbb006177c6117e4310ad182d15bdbc3aa6ed79

diff --cc src/gromacs/trajectoryanalysis/analysismodule.h
Simple merge

diff --cc src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index 912db6c9633ce7b530abc8cfa47fd645b1659da2,056d3ac5ef858ea810dbebc759cc0d573b9f48cd..6a8ebfef9d4aab29d649babe48e225f999a72290
--- 1/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
--- 2/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@@ -114,20 -114,12 +114,16 @@@ TrajectoryAnalysisCommandLineRunner::Im
  
      options.addManager(&fileoptManager);
      options.addManager(&seloptManager);
 -    IOptionsContainer &commonOptions = options.addGroup();
 +    if (full) {
-         options.addSubSection(&commonOptions);
++          IOptionsContainer &commonOptions = options.addGroup();
 +    }
-     options.addSubSection(&selectionOptions);
-     options.addSubSection(&moduleOptions);
+     IOptionsContainer &moduleOptions = options.addGroup();
  
      module_->initOptions(&moduleOptions, settings);
 -    common->initOptions(&commonOptions);
 +    if (full) {
-         common->initOptions(&commonOptions);
++          common->initOptions(&commonOptions);
 +    }
-     selections->initOptions(&selectionOptions);
+     selections->initOptions(&commonOptions);
  
      {
          CommandLineParser  parser(&options);
@@@ -138,10 -130,8 +134,10 @@@
          options.finish();
      }
  
 -    common->optionsFinished();
 +    if (full) {
-         common->optionsFinished(&commonOptions);
++          common->optionsFinished();
 +    }
-     module_->optionsFinished(&moduleOptions, settings);
+     module_->optionsFinished(settings);
  
      common->initIndexGroups(selections, bUseDefaultGroups_);
  

diff --cc src/gromacs/trajectoryanalysis/runnercommon.cpp
Simple merge