[Molecuilder-devel] [SCM] annotated tag v1.5.3 created. v1.5.3

[git at ins.uni-bonn.de]

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The annotated tag, v1.5.3 has been created
        at  b2fc1c7ae9ab022737fedf97e0205a4a23952928 (tag)
   tagging  a95f5d33525f59abab6d0c6c038124f19f3dce8f (commit)
  replaces  v1.5.1
 tagged by  Frederik Heber
        on  Thu Apr 28 20:09:46 2016 +0200

- Log -----------------------------------------------------------------
- QtGui now crashes only in 1-2% of all regression tests (new record).
- we copy all information regarding visual entities and regaring the displayed
  lists via QtObserved... instances or via central ..Observer entities.

This version contains the following branches:
a95f5d3	Candidate_v1.5.3
9d1a785	QtGUI_lastfixes (and more final fixes).
30b1340	GLWorldScene_lastfixes (some final fixes)
ea79260	GLWorldScene_stores_objects (All GLMoleculeObjects now are created by
	and belong to GLWorldScene)
d16a06c	Changes_due_to_changes (some subsequent changes)
a13f2bb	GLWorldScene_notes_parents (great GUI simplification: GLWorldScene just
	changes GLMoleculeObject_..'s parents when necessary)
785d890	NoPartialSpecialization_ObservedValue_wCallback (simplified
	ObservedValue)
96f14ae	Adding_QtObservedBond (QtObservedBond to copy info on bonds)
bf62452	QtObservedInstances_use_index_internally (QtObserved.. instances also
	use the new index for all its contained ObservedValues)
76c238d	QtObservedInstanceBoard_introducing_index (unique index of same type
	for all QtObserved.. instances)
bff202c	QtMoleculeList_MoleculeObserver (central MoleculeObserver that
	registers all changes to molecules)
bfd520c	QtElementList_AtomObserver (central AtomObserver that registers all
	changes to atom's elements)
14de9a4	Fix_BondsNotShowing (bonds were not shown in QtGUI)

Frederik Heber (181):
      World's ObservedContainer no longer observe.
      FIX: Fitting domain to window on QtMainWindow's init.
      FIX: World::destroy..() did not emit SelectionChanged signal.
      FIX: World needs to first destroy the molecule, then release its ids.
      FIX: not using const ref in binding updateBoundingBox() for molecule.
      Added recreateAtom() and recreateMolecule() to World.
      AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..().
      Added extra signal MoleculeChanged to AtomObservable.
      FIX: Added copy cstor for AtomicInfo.
      FIX: PotentialTrainer did not use user-specified threshold so far.
      Fit..PotentialAction now allow setting maximum number of optimization iteration.
      TESTS: Trimmed down PopMoleculesSelection regression test.
      TESTS: Trimmed down TREMOLO dbond regression test.
      LinkedCell's LinkedList is now a vector and no longer a set.
      FIX: PdbParser would calculate trajectors over all atoms, not just given set.
      FIX: Long-range forces were not added onto atom's forces.
      Added Cacheable MoleculeCenter to molecule which is cleverly updated.
      FIX: molecuilder.py is now loaded after GUI is done initializing.
      FIX: Fixed wrong paths for adjacency and trianglematcher in regression and GuiChecks tests.
      Added select() and unselect() functions to atom and molecule, also SelectionChanged channel.
      Added template functions to (un)set vector of instances in a row.
      FIX: AtomObserver was not up-to-date with respect to atom's channels.
      Added MoleculeObserver as pendant to AtomObserver for molecules.
      Extracted common code out of Molecule/AtomObserver into EntityObserver.
      Removed FindEmbeddingHole which lacked implementation so far.
      Replaced MoleculeListClass in analysis_bonds by vector of molecules.
      Replaced MoleculeListClass in ExportGraph by vector of molecules.
      Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase.
      Deleted MoleculeListClass.
      atom now uses associate... and disassociatedAtomWithMolecule().
      Molecule now has maps with old values for bond counts and element number per atom.
      Removed molecule's resetFormula() and doCountBonds() and doCountNoNonHydrogen().
      FIX: molecule's BoundingBoxSweepingAxis used unordered set of atomids.
      QtFavoriteActions uses ObservedValue for checking last queued action's name.
      FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box.
      FIX: GLWorldScene has additional moleculePrepared... slots and signals.
      FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver().
      FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector.
      FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet).
      FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly.
      GLMoleculeObject_molecule's ObservedValues is now all static.
      GLMoleculeObject_atom's ObservedValues is now all static.
      GLMoleculeObject_bond's ObservedValues is now all static.
      Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter.
      Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface.
      FIX: QtMoleculeItem not signing off after subjectKilled().
      GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene.
      Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule.
      Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard.
      Added QtObservedAtom and ..Molecule() instances.
      Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard.
      Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer.
      Extracted all ObservedValue functionality out of GLMoleculeObject_atom.
      Extracted all ObservedValue functionality out of GLMoleculeObject_molecule.
      Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer.
      ObservedValuesContainer now stores QtObserved.. instances directly.
      FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff().
      Added AtomCount and FormulaChanged to QtObservedMolecule.
      All QtMoleculeItem now heed QtObservedMolecule and QtMoleculeList takes InstanceBoard.
      Removed molecule's AboutToBeRemoved channel.
      Extended QtObservedAtom by Name and Molecule.
      Extended QtObservedMolecule by Center, NonHydrogenCount, and BondCount.
      QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues.
      FIX: All ObservedValue getters now return const references.
      Equipped QtInfoBox with mutex and split clearTabs().
      FIX: Qt's parent properly set from QtMainWindow's point of view.
      QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback.
      FIX: ObservedValue need to be removed with a bit of delay.
      QtInfoBox disconnects signals.
      FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from World.
      Added ObservedValue for selection status of atoms and molecules to QtObserved...
      Removed QtSelectionUsage in GLWorldView and related.
      Removed QtSelectionAgent usage in QtMoleculeListView.
      Removed QtSelectionChangedAgent.
      FIX: ObservedValuesContainer uses deque for internal observed values.
      FIX: ObservesValuesContainer uses internal struct for two iterators for observedvalues.
      ObservedValuesContainer now asserts that observedinstance has been requested at least once before deletion.
      QtMoleculeList must not use QtObservedMolecules in lists but only request them on need.
      CHECK: tempcommit: Removed Cacheable of TesselationHull for GLMoleculeObject_molecule.
      GLMoleculeObject_atom and .._molecule don't get QtObserved... right away.
      CHECK: Don't admonish empty missed states in GLWorldScene?
      QtElementList must not use atom but only QtObservedAtom.
      FIX: Added mutex to ObservedValuesContainer to ensure atomic access.
      Combined checks into checkRemoval() in ObservedValuesContainer.
      QtObservedInstanceBoard now sends QtObserved..::ptr around in signals.
      QtObserved... now count the subjectKilled() from the containes values.
      FIX: indexChanged from QtObserved... transmit both old and new id.
      FIX: Making sure that atomInserted is received from same source in GLWorldScene and GLMoleculeObject_molecule.
      FIX: GLMoleculeObject_.. does not care whether selection state did not change.
      All ..Inserted/..Removed signals now go through GLWorldScene.
      Removed RefCounted... again.
      GLWorldScene places GLMoleculeObject_molecule into extra list before removal.
      AtomInserted/Removed of QtObservedMolecule sends ptr as unique key.
      tempcommit: Removed atomDelayed stuff in QtObservedInstanceBoard's header.
      Removed last...removed in QtObservedInstanceBoard.
      SignedOn_t in QtObservedInstanceBoard is again just a set.
      FIX: GLWorldScene's moleculesAtomRemoved was checking QtObservedAtomMap.
      GLWorldScene RemovedMolecules now uses QtObservedMolecule* as key.
      FIX: emit changed signal before moleculeEmptied.
      FIX: QtObservedAtom's AtomMoleculeIndex was not informed of molecule index changes.
      GLWorldScene also takes note of empty molecule.
      Enhanced documentation for Qt constructs.
      FIX: Renamed FitParticleCharges -> FitPartialCharges.
      Added regression test for fill-regular-grid that with minimum distance.
      FIX: Filling actions did not use minimum distance for tesselated surface.
      Brought GuiChecks up to speed again.
      DISTFIX: Added AdjacencyMatcher and TriangleMatcher noinst targets.
      TESTFIX: Needed to check whether long-range capability is compiled in.
      Set version to 1.5.2.
      Half of the bonds are showing up again.
      FIX: GLMoleculeObject_atom did reset position not bonds on bondsChanged.
      FIX: QtObserved... did not destroyObservedValues() so far.
      GUITESTS: Decreased waiting times in QtGUI's test mode.
      All QtObserved..::update..() now use the atom or molecule ref instead of index getter.
      Added getObserved..() functions to QtObservedInstanceBoard that take Observable.
      Moved QtElementList into own subfolder.
      QtObservedAtom and ..Molecule now have internal selfref.
      Added QtObservedAtomObserver to ElementList subfolder.
      QtElementList uses QtObservedAtomObserver and is no longer Observer itself.
      FIX: molecule did not notify about FormulaChanged at the right moments.
      FIX: molecule::SetNameFromFilename did not notify about MoleculeNameChanged.
      Added QtObservedMoleculeObserver that relays signals on all QtObservedMolecule's.
      Removed emitDirtyState callback from QtMoleculeItem.
      Removed QtMoleculeList::informDirtyState(), callback is not needed anymore.
      Removed all mutexes and updateDirtyStates() in QtMoleculeList, replaced by simpler slots.
      QtMoleculeItemFactory is pure static.
      FIX: QtMoleculeList::moveItem() does not need to search for groupitem.
      QtMoleculeItems do not store ObservedMolecule::ptr any longer.
      Added missing updateState() to QtMoleculeList.
      FIX: QtMoleculeList's FormulaVisibilityCountMap was not inserted into on new group item.
      Introduced unique and permanent ObservedValue_Index_t.
      Added convenience function to return current id for given index.
      QtObserved...Observed now get index on ...Removed() signal.
      MoleculeList discerns between internal and external name change.
      Changed slots of GLWorldScene and GLWorldView.
      FIX: Removed some unnecessary observer code from GLWorldView.
      Removed GLMoleculeObject_molecule::getPresentAtoms() and changed atomRemoved slot of GLMoleculeObject_molecule.
      Removed unneeded specialization ObservedValue_UpdateAtoms.
      FIX: QtObservedMolecule::initObservedValues was still static.
      QtObservedAtom uses new index internally.
      QtObservedMolecule also uses new index internally.
      FIX: Removed GLMoleculeObject_molecule's molref.
      Added QtObservedBond, managed by QtObservedInstanceBoard.
      Modified all GLMoleculeObjects and GLWorldScene to the new QtObservedBond.
      Removed partial specialization of ObservedValue_wCallback for index.
      getObserved...() checks whether id is still present.
      QtObservedBond now simply gets both QtObservedAtoms on construction.
      FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
      Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.
      QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
      QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
      GLWorldScene now properly reassigns parents of GLMoleculeObjects.
      FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.
      FIX: made disconnect() check for NULL pointers.
      QtObservedAtom uses fixed index which it returns.
      QtObservedBond uses fixed index which it returns.
      QtObservedMolecule uses fixed index which it returns.
      FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
      GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
      GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
      FIX: MoleculeList crashed when selected molecule changed its place.
      FIX: Empty row in QtMoleculeList was not deleted.
      FIX: ObservedValue_Index_t is now the memory address of the Observer instance.
      Added checks abd verbosity to reparenting in GLWorldScene.
      QtObserved... signals indexChanged does not transmit ids anymore.
      QtObservedBond returns ::ptr instead of ptr from left and right atom.
      FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.
      GLWorldScene needs to store observed values to ensure duration of their lifetime.
      GLWorldScene removes stored observed values only after both parent is NULL and atomRemoved() came in.
      GLWorldScene now holds onto atoms and bonds until ..Removed() signal and parent(s) is reset.
      Protecting access to atom and bond functions in GLWorldScene with mutexes.
      Split ObservedValueIndexLookup such that it is protected under atom or bond mutex.
      Made GLWorldScene::resetParent() safe for multiple threads.
      FIX: molecule returned BondCount twice as large.
      FIX: GLWorldScene::removeBond() needs to check whether molecule changed already.
      FIX: PdbParser scanned through all present atoms once per ATOM line.
      QtObservedInstanceBoard::get..ToIndex() now serve -1 as illegal id when index not found
      FIX: QtMoleculeList has flag to tell when nameChanged came from outside.
      FIX: QtMoleculeListView::rowsSelected() checks for illegal id from get..ToIndex().
      FIX: GLWorldScene used iterator also in NDEBUG, connect still outside mutex.
      Set version to 1.5.3.

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