[Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.8 created. v1.4.8

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The annotated tag, v1.4.8 has been created
        at  c6204d0e3a45cbcb6116e4a45ea9853eba248be5 (tag)
   tagging  7f6a2fc9f64c88371654df745552167f0e0e3a9c (commit)
  replaces  v1.4.7
 tagged by  Frederik Heber
        on  Wed Sep 17 21:39:28 2014 +0200

- Log -----------------------------------------------------------------
Valgrind-checked the code and eliminated all memory leaks.
First step of cleaning out old code (molecuilder_geometry and old fill Actions)
GUI is a lot more useful (empty dialogs do not show up, i.e. easy clicking with
	all selection actions, undo/redo, ..., bonds are properly updated when
	atoms move, tooltips for every option in dialogs, homology tab working,
	suffixes as filters in filedialogs)

This version contains the following branches:
7f6a2fc	Candidate_v1.4.8 (Fixes after merge and version)
8859b5e	GUI_Fixes (Lots of fixes to ease and enhance GUI usage)
5a9f4c1	Cleanup_old_code (throwing out old pieces of code, especially filler)
5524ae9	MemFixes (enable-valgrind now runs through without a glitch (except
	Python-related regression tests))

Frederik Heber (54):
      FIX: Process' dstor would always stop() even if not start()ed.
      FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access key_end().
      FIX: Box::setM() did not use const ref as argument.
      FIX: regression test add atoms outside boundary had given boundary conditions wrong in arguments.
      FIX: Made checks in random number engine and distribution regression tests more robust.
      MEMFIX: World's homologies not deleted.
      MEMFIX: Mismatched delete in PdbParser::Save().
      MEMFIX: ActionQueue would loose memory when action failed.
      MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked memory.
      MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate.
      MEMFIX: PotentialRegistry's dstor forgot cleanup().
      MEMFIX: PartialNucleiChargeFitter lost memory.
      MEMFIX: Many analysis_correlation function allocated return map twice.
      MEMFIX: Tesselation::operator() did not free linkedlist.
      FIX: molecule::Translate() uses AtomSet directly.
      Added option keep-bondgraph to MolecularDynamicsAction and StructuralOptimizationAction.
      World::setTime() now only copies bond graph, does not re-create it.
      FIX: Removed some misleading output of CorrectBondDegreeAction.
      FIX: BondGraph::cleanAdjacencyList() killed bonds of time steps before.
      FIX: GLMoleculeObject_shape might use empty point list for tesselation.
      FIX: Added update mechanism to GLWorldScene when WorldTime changes.
      FileQtQuery retrieves valid suffixes from validators.
      FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector().
      FIX: Changes to function signatures in molecule_geometry.
      Added FileSuffixValidator to all Actions where missing but appropriate.
      In QTUI empty dialogs no longer have to be confirmed.
      FIX: Querys now have own description as tooltip, not Action's.
      In QTUI Dialog window now has a meaningful title.
      QMenu extended for tooltips, but not working yet.
      FIX: new item is just to some default values in QtMoleculeList, filled later anway.
      FIX: FillRegularGridAction requires filler molecule at origin.
      Extracted filler preparing functionality from FillRegularGridAction.
      FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/.
      Added FillVolumeAction for filling a Shape's volume.
      Refactored FillSurfaceAction to also use FillerPreparators.
      Removed FillVoidWithMolecule and FillWithMolecule actions.
      Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions.
      Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction.
      Removed PrepareClustersInWater().
      Removed lots of commented-out code from GLWorldView.
      FIX: QtQueryList now works with pointers, FileQtQuery gives name of file.
      FIX: QSeisPlotPage takes up all remaining space in QtHomologyList.
      FIX: QtHomologyList lacked use of FunctionModel::filter_t to split up arguments.
      Made ActionQueue observable.
      Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions.
      MEMFIX: ActionQueue was not stopped() when argument parsing failed.
      MEMFIX: ElementDbAction would loose memory when parsing command-line arguments failed.
      DOCU: Update on test policy with respect to now working valgrind tests.
      Merge branch 'Cleanup_old_code' into stable
      Merge branch 'MemFixes' into stable
      Merge branch 'GUI_Fixes' into stable
      MEMFIX: Thrown ParserException causes mem leak in LoadAction
      FIX: CommandLineParser causes idling thread when parsing goes wrong.
      Set version to 1.4.8.

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