<bugfix>keep selected modules after scene redraw</bugfix> <bugfix>Optional input ports now don't show up as output ports</bugfix>
<bugfix>keep selected modules after scene redraw</bugfix>
<bugfix>Optional input ports now don't show up as output ports</bugfix>

gui/pipeline_view.py:
  - QGraphicsModuleItem.setupModule: split visibleOptionalPorts into
    input and output lists
  - QPipelineScene.setupScene: isSelected -> isSelected(), and then
    call setSelected on the selected modules at the end

VisTrails/VisTrails,celiafish/VisTrails,Nikea/VisTrails,hjanime/VisTrails,hjanime/VisTrails,minesense/VisTrails,Nikea/VisTrails,minesense/VisTrails,Nikea/VisTrails,hjanime/VisTrails,VisTrails/VisTrails,hjanime/VisTrails,celiafish/VisTrails,celiafish/VisTrails,minesense/VisTrails,celiafish/VisTrails,VisTrails/VisTrails,minesense/VisTrails,hjanime/VisTrails,minesense/VisTrails,VisTrails/VisTrails,Nikea/VisTrails,VisTrails/VisTrails