From git at ins.uni-bonn.de  Sat Oct 31 10:37:44 2015
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Date: Sat, 31 Oct 2015 10:37:44 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] branch
	Fix_QtGui_Testmode_not_showing_atoms created. v1.5.0-149-g65a7318
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The branch, Fix_QtGui_Testmode_not_showing_atoms has been created
        at  65a73184853e7894f8c1ba485eb4be5aeadc8673 (commit)

- Log -----------------------------------------------------------------
commit 65a73184853e7894f8c1ba485eb4be5aeadc8673
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 19:56:03 2015 +0100

    Revert "Added mutex to QtObservedInstanceBoard."
    
    This reverts commit d6047811a42782cb37d49830bc6e17d3b3344f68.

commit 9f3f9e56a581dc70fb89d4d5c805a1b9133fa9b1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 19:55:42 2015 +0100

    Revert "tempcommit: QtObservedInstanceBoard uses mutex only for subjectKilled(). Merge with d6047811"
    
    This reverts commit 039eb1d53b41317c75d39a6563658582140d83d2.

commit 039eb1d53b41317c75d39a6563658582140d83d2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 18:43:21 2015 +0100

    tempcommit: QtObservedInstanceBoard uses mutex only for subjectKilled(). Merge with d6047811

commit 08f75432db31263ed75f1e0313881f79ad1d3669
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:41:51 2015 +0100

    tempcommit: Merge with e228f3

commit 1832dcfa09ffeb5afd0995ea16cd9f9184e55c80
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:26:57 2015 +0100

    tempcommit: Merge with 5aa1f2b7

commit 8d7fd984e57ad3b7f731ae516575b5d5d6c07f11
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:18:41 2015 +0100

    tempcommit: Merge with e228f3

commit d6047811a42782cb37d49830bc6e17d3b3344f68
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:17:46 2015 +0100

    Added mutex to QtObservedInstanceBoard.

commit e228f3ba9206ecc217c85ae73ee38e5d4c708fc5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:15:30 2015 +0100

    TODO: QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback.
    
    - due to Qt's signal/slot destruction, which follows no proper order,
      we need to invalidate callback when their owners are destroyed. Each has a
      note-function() that flips the boolean to show the callbacks invalidity.
    - TODO: So far this is not nice, especially w.r.t to ObservedValue_wCallback
      because of templatization. We cannot place them in a loop and this makes
      this very error-prone once more Values are added ...

commit d96f9a55c651a1c31a14cdd2b670739c244a4ef2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:14:57 2015 +0100

    tempcommit: Need to split signedOn maps for atoms and molecule due to different number of channels. Merge with ...?

commit dc05d81bfe40be3c1ebfc4fec8f0305adce08217
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:13:33 2015 +0100

    tempcommit: merge with eda203c3

commit b47afb72fab6df9dcd5f84cae5ac3d29800413bf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 17:07:39 2015 +0100

    FIX: Qt's parent properly set from QtMainWindow's point of view.

commit 73fcc4d0eb85a7339453cb79a5421a0bd595b392
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 16:58:50 2015 +0100

    Revert "DROPME: Removed logging into QtLogBox for debugging."
    
    This reverts commit 57b9cd365da71ff1d62c3ce6c112e331b086289f.

commit 6e03cac48ca5729cfedfe279432bada76497baf6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 15:14:07 2015 +0100

    tempcommit: merge with a8c9551b

commit eda203c3214c9cbf233c4820cd727a0f39a8d658
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 15:07:55 2015 +0100

    tempcommit: Equipped QtInfoBox with mutex and split clearTabs().
    
    - this avoids a memory corruption with signal/slots as the first atomRemoved()
      signal also removes the molecule and hence the QtObservedMolecule ptr who
      is the recipient of the subsequent moleculeRemoved() signal.

commit e54456aae6e9d661d577a0d9c7f05cef7b339b51
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 15:07:41 2015 +0100

    tempcommit: merge with 70c61bd4+

commit 571fcbfee2a325e073fcd5a0547bb3ade866c384
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 12:54:29 2015 +0100

    FIX: All ObservedValue getters now return const references.
    
    - this should avoid some unnecessary copying.

commit 271060fcd1c1de868a06b88d8f1e34baece52521
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 12:36:21 2015 +0100

    FIX: molecuilder.py is now loaded after GUI is done initializing.
    
    - otherwise consequences of loaded session (atoms, ...) are not displayed.
    - originally, this was done on purpose as it is quicker to just load stuff into
      the world and then tell the GUI to show what's there. However, now, due to
      constraints with different threads, this is no longer possible.

commit 95a757bd9e1a5660ed590dc64a0503195ee32596
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 12:35:53 2015 +0100

    tempcommit: Merge with 7a8832d4

commit 12ecc9a464e868e2095278c8287986ee5b0f9b4d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 12:06:30 2015 +0100

    QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues.

commit 785fde32fe13558ebf6870591ef8b9152f0a93bf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 12:06:14 2015 +0100

    tempcommit: merge with 7a8832d4

commit 5aa1f2b7ccecfee7e1238002ab0885590c9d3791
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 11:49:06 2015 +0100

    xtended QtObservedMolecule by Center, NonHydrogenCount, and BondCount.
    
    - added Cacheable MoleculeCenter to molecule which is cleverly updated.

commit 7a8832d4d20ecc2d2ff1aed5d2ca5f66be24695a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 11:48:16 2015 +0100

    Extended QtObservedAtom by Name and Molecule.
    
    - added extra signal MoleculeChaned to AtomObservable.

commit 834ff2cd2cd7749afa723eb22f681f2722b342ff
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 30 00:11:39 2015 +0100

    tempcommit: Merge with 087563d29

commit abc9ea4cdbe2032f5fe794618b80a6a7d9513b91
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 23:52:15 2015 +0100

    tempcommit: merge with 74d1bd0

commit 087563d292ebfaff5e237b4898d8a1fce4023cdb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 23:22:53 2015 +0100

    QtMoleculeList takes InstanceBoard and listens to its molecule signals.

commit 74d1bd00b1401eb63c10b46a6a2b67f7132db9f4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 23:21:30 2015 +0100

    All QtMoleculeItem now heed QtObservedMolecule.
    
    - QtMoleculeItems no longer use Observer/Observable but get updates via
      signal/slot from QtObservedMolecule.

commit 6356a6059f318b7bd416858a363d7a283b456aa1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 22:55:51 2015 +0100

    Added AtomCount and FormulaChanged to QtObservedMolecule.

commit 3b881145335c6ff16050bf12b91a96fe28d29684
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 19:45:46 2015 +0100

    tempcommit: merge with 1c293cec

commit 672945f5568c3592c37bee33145d3a62a7d0e091
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 19:45:22 2015 +0100

    tempcommit: merge with 0fb2d3c3

commit 7d8b8b43517de6849f3bb430ad05db0059e990c6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 19:38:02 2015 +0100

    FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff().

commit 0fb2d3c39f1eab131b6ee8cfcc9fca9f9f7ced38
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 19:31:07 2015 +0100

    Revert "QtObserved..::AllSignedOnChannels is needed statically."
    
    This reverts commit 080cc49c388944e7782fa8e00e79b58a16b75974.

commit 8bc85f6767371493ec33741f717bb09f9d89fbde
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 19:30:33 2015 +0100

    tempcommit: Merge with 70c61bd4

commit a345227a313fe74b7e6b9f511ca909664fe97b2a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 17:22:46 2015 +0100

    tempcommit: Merge with a8c9551b

commit 9e007daf870bfbcf45ef770c4621e818439e3585
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 17:20:24 2015 +0100

    tempcommit: Fixing signals of QtObservedMolecule. Check and merge with 92a780a

commit 6c6d3c2df81a2c98c86f7475b5131dc955d5187c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 17:17:34 2015 +0100

    tempcommit: activateObserver needs to be called after insertion into ObservedValuesContainer. Merge with c0943f48

commit 9881c3b93ce026abf818cdb1eb54905ac2bd65f2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 17:16:49 2015 +0100

    tempcommit: Added again check on lastremoved.. to InstanceBoard.

commit 080cc49c388944e7782fa8e00e79b58a16b75974
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 17:15:40 2015 +0100

    QtObserved..::AllSignedOnChannels is needed statically.
    
    - this is used to check whether all ObservedValues already had their
      subjectKilled() called.

commit b775b7ab9e68e656ce1078acbca5bd80429d9829
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 16:26:13 2015 +0100

    tempcommit: Merge with ad571e28

commit f50b98a0d968216c12648ab5b3d71845dc55df6c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 16:26:02 2015 +0100

    tempcommit: Merge with 5a7b4a23

commit 8b16324d3cf9be7dbdf92a601c4c3a67c3297b0d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 16:24:15 2015 +0100

    tempcommit: Merge with c0943f48

commit ad571e284a59bf54e939d7a4a3025466f30381f5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 16:23:18 2015 +0100

    tempcommit: Merge with a8c9551b

commit 5a7b4a23d77105c2b2ad6d3cf83663c33cd8834a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 16:22:44 2015 +0100

    tempcommit: Merge with 92a780aa

commit 70c61bd41e1e139d3f3e552ed794aa741c736325
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 16:12:34 2015 +0100

    No more ObservedValues_t from QtObservedInstanceBoard.
    
    - we now work with QtObserved..::ptr directly everywhere.

commit 89a166473561b51e254c1cb815611d71c4726d11
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 15:46:17 2015 +0100

    tempcommit: merge with e6d34be3

commit c0943f48129c534587407d263d59cb56aa9a836d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 15:41:13 2015 +0100

    ObservedValuesContainer now stores QtObserved.. instances directly.
    
    - we need this as QtObservedAtom and ..Molecule must signOn() to World's
      instance right away. If later requests to ObservedValuesContainer::get()
      cause new signOn()s, then these might fail.

commit e6d34be30f840209719f7a0075f29dfbbca6529c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 15:02:35 2015 +0100

    Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer.
    
    - this avoids some more duplicated code.

commit a8c9551b45087863cb04b87bdf54ffd64ded6f08
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 13:52:29 2015 +0100

    Extracted all ObservedValue functionality out of GLMoleculeObject_molecule.
    
    - see previous commit for explanations.

commit 92a780aa795996a1d3bd79a2083b2794115b3782
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 11:46:45 2015 +0100

    Extracted all ObservedValue functionality out of GLMoleculeObject_atom.
    
    - i.e. GLMoleculeObject_atom is reduced to simple displaying, updated via
      Qt signals. These signals are connected to a QtObservedAtom which in turn
      now contains all the ObservedValue functionality.
    - this is preparatory for having a single (Observed)Atom as representer of
      its associated World's atom in the QtGui part of the code.

commit 2f158c56623234be6ebfbc278761bd440773f715
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 29 10:52:10 2015 +0100

    Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer.
    
    - this avoids a lot of code duplication.

commit 76d18f39134465d8a544751f9e36f6cc11e3cbed
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 14:57:10 2015 +0100

    Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard.

commit 6a50bb20ea7ea1b24f4ffac1990bc37d9078d426
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 14:24:10 2015 +0100

    Added QtObservedAtom and ..Molecule() instances.

commit 1c293cecf80bebccd7bd90664c05f0aae700e3c9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 14:23:09 2015 +0100

    Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard.
    
    - this is preparatory for adding ObservedAtom and ObservedMolecule classes
      that combine all observed information on either type.

commit 066f19447803d0bf7000ac80c17ecbfe55c290e0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 13:09:43 2015 +0100

    AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..().

commit a869e049c07be3cf8a6950d3b1bf73b71c6cdf7a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 13:08:04 2015 +0100

    Added recreateAtom() and recreateMolecule() to World.
    
    - in order to overcome problems with Qt signals being delayed so much that
      in between sending and receiving the id of a newly instantiated atom has
      changed, we need to set the right id (after undo/redo commands) right
      away. For this, these two new functions are well-suited.

commit e8cb76a185c93938c78d43387229180d20fe6e07
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 10:20:53 2015 +0100

    GLMoleculeObject_molecule does not listen directly to molecule::AtomInserted/Removed.
    
    - this is done by QtInstanceInformationBoard instead.

commit 0e8af80722e2f47e6b65e77c8cb0ad1abc12b91d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 10:20:09 2015 +0100

    QtInstanceInformationBoard has now unique maps for either set of ObservedValues.

commit 97bb26d4907d865970184db65245b6070b7da9d7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 28 10:13:15 2015 +0100

    FIX: GLMoleculeObject_atom and .._molecule need to account for multiple subjectKilled(), one per channel.

commit 338e3a86a7595d963f667cbaef3c44f38063e4e1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 20:51:05 2015 +0200

    Revert "tempcommit: Removed a lot of now unused signal/slots from World, Scene and _molecule."
    
    This reverts commit 61b8538c5cad80c1af7db190009b1406dcb696f9.
    
    Conflicts:
    	src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp
    	src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp
    
    - readded MissedStateMap in GLWorldScene.

commit 9d7f587da43870b91b2e6990586cb2c461b42126
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 20:28:45 2015 +0200

    tempcommit: QtInstanceInformationBoard informs about AtomRemoved, AtomInserted via molecule.

commit 7547a3be8fd2121c65b2ddeb5df6d377924c8cfa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 20:28:23 2015 +0200

    tempcommit: Selection uses direct connection.

commit 4445f7735e8e685a8e8b404e73ce91f85bda383f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 20:27:50 2015 +0200

    tempcommit: Removed resetAtoms() and PresentAtoms from GLMoleculeObject_molecule.
    
    - this information must come from instanceboard.

commit 4c6952672301696fa7fc10a169afa9a97e67fc2c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 19:20:40 2015 +0200

    QtInstanceInformationBoard also informs about index changes.

commit 2b65b4846cdb14011409001d8870719c72973a77
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 19:20:13 2015 +0200

    tempcommit: GLMoleculeObject_atom uses resetBonds() to add initial bonds.

commit e962bf24ac918adb591a550e600008d9efa4ccfa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 18:48:19 2015 +0200

    tempcommit: .._atom and .._molecule now return ObservedValue to QtInstanceInformationBoard.
    
    - this way we can transfer these from one GLMoleculeObject_atom to another.

commit 61b8538c5cad80c1af7db190009b1406dcb696f9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 18:47:31 2015 +0200

    tempcommit: Removed a lot of now unused signal/slots from World, Scene and _molecule.
    
    - basically all replaced by QtInstanceInformationBoard connections.

commit 58737c96ffae94195696088c0a78976c1aaa8451
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 18:46:36 2015 +0200

    tempcommit: Removed countSubjectKilled() and deprecator cstors from .._molecule.

commit dc5c8f72db61ba5a149ede2a997a1a3c40528e63
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 18:45:21 2015 +0200

    tempcommit: Removed countSubjectKilled() and deprecated cstors from .._atom.

commit 8fd310cf6a723b7458fb7aa2e46c971fb3cefb7a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 18:03:53 2015 +0200

    tempcommit: QtInstanceInformationBoard signOn maps need to store ref, not id. Merge with ...
    
    - we cannot access atom's id as only AtomObservable is left.

commit 664d3ee7336ae4219f5826083bc628b676796504
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:21:37 2015 +0200

    tempcommit: not using const ref in binding updateBoundingBox() for molecule.

commit 57b9cd365da71ff1d62c3ce6c112e331b086289f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:21:16 2015 +0200

    DROPME: Removed logging into QtLogBox for debugging.

commit 9e0a33ac8bdd6947c0a04fd73187cea4b68a2722
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:20:56 2015 +0200

    tempcommit: Additions to DROPME: debugging output. Merge with ...

commit ca20d7b996c43666281013354bd200c6451dea86
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:20:34 2015 +0200

    tempcommit: Fixes to QtInstanceInformationBoard. Merge with ...

commit 2a1fa1f4859c41480232bbf66ef1af0a0031927b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:19:46 2015 +0200

    tempcommit: Merge with e84e2c80

commit d77744bf3b3c4edca89a7d4346166d0e9fcd01e4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:18:13 2015 +0200

    DROPME: Added debugging output to QtInstanceInformationBoard.

commit 72cd6215eed6def5c3c4d89e5df800e7684d088f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:17:43 2015 +0200

    FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet).

commit e0ff31fa724d04612bcaa4b652b1bfbb80ba9ad1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:17:19 2015 +0200

    tempcommit: resetTesselationHull() only called when owner still present.

commit 44d90cfbf4c0582186c8158941c0d02978b92f08
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:16:53 2015 +0200

    Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule.

commit ce326e15d9e99bbab30b4772cb336a3c5d2fa7a7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:16:30 2015 +0200

    GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene.

commit a7a81684ba0cf49e1bd43c0272a542de73424dce
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:13:14 2015 +0200

    FIX: QtMoleculeItem not signing off after subjectKilled().

commit 36f72a26eff131507efec4b9d4668ab086fd7d8a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 23 17:12:42 2015 +0200

    tempcommit: QtInstanceBoard lifetime managed by parent QtMainWindow. Merge with ...

commit 1c50baf9829a26f204938f7c6f0db62ccf17c719
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 21:46:52 2015 +0200

    tempcommit: Replaced connections GLWorldView with QtInstanceInformationBoard.

commit bf1de432c42165753bd9c996bd2b5e4b5cfb6205
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 21:08:44 2015 +0200

    tempcommit: Enhanced ObservedValue_wCallback to take a bound getIndex function().
    
    - additionally, we route internally to ObservedValue::get() and this gets us
      out of the painful situation where we need to supply an index getter to the
      ObservedValue that monitors the index (and hence must be present already to
      bind to its get function).

commit e84e2c80597cedd0d64825fb5cef8b951359c789
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 19:03:48 2015 +0200

    tempcommit: Final version of QtInstanceInformationBoard.

commit cc861e0f1fcce8aaf29d231e672495d718a48949
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 19:01:09 2015 +0200

    Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter.
    
    - this is a precursor for when the ObservedValues reside with
      QtInstanceInformationBoard.

commit 57d3ae2e8eb2070b76bae18e2b6c05b89b6cf2c4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 18:59:19 2015 +0200

    tempcommit: Merge with f6e0c328

commit 0a0cbe536dd01a4864f68d9b4cb39942f20c4ff1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 18:58:32 2015 +0200

    tempcommit: Merge with 96d38bf

commit 33bdeff78e8289331e8eea760bb818e6fd13ab17
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 18:57:48 2015 +0200

    tempcommit: Merge with af7a33c5

commit 59c1c6f8b33a2deceab5c6d8263f5e9fd8744c9f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 18:47:35 2015 +0200

    temcommit: Merge with f6e0c328

commit 2683c18da13ba37c11a576121ca65c72bfa4944a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 17:42:17 2015 +0200

    Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface.
    
    - this is meant as a instantiator of all ObservedValue's needed by QtGui for
      representing information from the World. The ObservedValue's are instantiated
      separately w.r.t. to the instance for the visual representation. This is
      light-weight and can be performed in the same thread, while the visual
      representation's instantiation can be done elsewhere and there we just need
      to access the ready ObservedValue's that exist as long as they are needed
      by the QtGui.

commit 085a87610d66db8fb9e578b0a11501791051478c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 17:41:24 2015 +0200

    tempcommit: Merge with f6e0c328

commit ed08e1426da5dcaaf57c69953f8349e21fe4999f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 17:41:01 2015 +0200

    tempcommit: Merge with af7a33c5f

commit 96d38bfd524a4e0eaa1d48ca99c0bb32673fcf61
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 15:28:19 2015 +0200

    GLMoleculeObject_bond's ObservedValues is now all static.
    
    - again, the same change as with .._molecule and .._atom.

commit af7a33c5f26d7efcc83ad69bd3f59333751ca04e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 14:55:30 2015 +0200

    GLMoleculeObject_atom's ObservedValues is now all static.
    
    - this is equivalent to the changes to GLMoleculeObject_molecule.

commit e9c2370056ed4e15d17f470f44487b1b4300be62
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 14:42:13 2015 +0200

    FIX: World needs to first destroy the molecule, then release its ids.
    
    - this is similar to the change for the atom.

commit f6e0c32812b93f7790837a0e033ab7be689ede42
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 14:40:14 2015 +0200

    GLMoleculeObject_molecule's ObservedValues is now all static.
    
    - this is preparatory for extracting their instantation to an external class
      InstanceInformationBoard that keeps track of the lives of instances in the
      World that are needed inside QtGui (e.g. for visual representation).

commit 190990ab5eb8412c3ce3d49cbdde37d18de10e19
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 14:18:30 2015 +0200

    FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly.
    
    - we need an old and a new set, i.e. the difference needs to be discernable
      between updates. However, so far we updated the old set directly, too.

commit c6f7d851f7c828041d233968209abd07c53b0eb2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 17 11:09:07 2015 +0200

    DROPME: Switching to log tab in worldTab for test-single.

commit cfcbd701acc2c2d72b56189edae70c870bce4819
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 16 21:48:20 2015 +0200

    FIX: World::destroy..() did not emit SelectionChanged signal.

commit 01ee257b96b3aa8d62e48dfae817ae0ab653c9c7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 16 13:51:16 2015 +0200

    FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector.
    
    - the idea is that a GLMoleculeObject may only remove itself _after_ each and
      every contained Observer has gotten the subjectKilled() signal from the
      Observables. Only then will destroying the Object and its members thereby
      not cause any signOff() which try to access Observables or their channels
      which are no longer present. This can be imagined as a graph where we have
      to start destroying object at the very bottom.
    - This is the avoid the following conflict: A superior object gets note of
      a molecule to be removed. It sends the visual representation a signal to
      remove itself, which causes it to use signOff(). On a parallel track (in
      another thread) we have the observed object calling subjectKilled() to
      inform any Observer about its immediate destruction. These two tracks
      collide. Now, we let first pass all subjectKilled() and when the last
      Observable has gotten its signal, we begin destroying the visual rep.
    - rerouted signal/slots accordingly.

commit d0225f4933595168bf533fabce90f7d419db754a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 16 10:59:22 2015 +0200

    FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver().
    
    - we just take note that we are signedOff.

commit 568a2ce22f8ef6124b26c0e1d410ebc7af6cff91
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 16 10:58:31 2015 +0200

    FIX: GLWorldScene has additional moleculePrepared... slots and signals.
    
    - i.e. we first insert into MoleculesInMap via direct connection and then
      signal is emitted (queued) to construct the actual GLMoleculeObject_molecule.

commit 5e96c742ba17709d74218898f5f708dbbf5228bb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 16 10:56:48 2015 +0200

    FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box.
    
    - we don't longer need the hack as we have the molecule cleverly updating the
      box and an ObservedValue.

commit d9ca9621d208e1af1fdaf75e5e2c1b5022e8e459
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 15 11:08:37 2015 +0200

    QtFavoriteActions uses ObservedValue for checking last queued action's name.

commit 35ccc012ef350e6eb15b273b40f361af989bc6ae
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 15 11:08:09 2015 +0200

    tempcommit: FIX: ActionQueue was setting lastchangedaction twice. Put into Fix_ActionQueue... branch

commit f7a37da6c306abfadb52abc833485cdeedf65874
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 14 11:18:05 2015 +0200

    FIX: Fitting domain to window on QtMainWindow's init.

commit 405dc5ea68d53a7ed220e143bb0dfe7082866028
Merge: 14a618b 62d092e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 13 22:14:45 2015 +0200

    Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.2

commit 62d092e08dbdb67e4f00547587c38322bf8bb828
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 9 00:12:20 2015 +0200

    Rewrote ChargeSmearer to use visitor pattern.
    
    - this is used for going over the bspline domain.
    - we need it when the support does not fit onto grid and when we need to
      recalculate the normalization.

commit 17e4fde191dda907bf7bd206803886c13e02d440
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 7 21:03:37 2015 +0200

    Added new option DoSmearElectronicCharges to FragmentationAutomationAction.
    
    - this uses ChargeSmearer: is prepared in InterfaceVMGJob and used in
      WindowGrid_converter.
    - VMGJob and VMGFragmentController need to pass along the DoSmearCharges option
      from the command-line.

commit 445ce6d3846182eaf130a6a73ea863d0a443e6f0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 7 08:25:28 2015 +0200

    Modified WindowGrid_converter::addWindowOntoGrid(): first reset, then write values.
    
    - this is required for smearing electronic charge distributions as we then
      write also neighboring values.

commit cceb8cfe148cf346613694b5f15bde9f95e63393
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 2 11:16:58 2015 +0200

    Added ChargeSmearer that is only compiled for CONDVMG.
    
    - we store the spline values in a singleton such that they are calculated only once.

commit 92232f71902106c7de16c1208aa802471f88fbb1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 11 16:14:00 2015 +0200

    Adding warning when inter-distance is given less then minimum required rcut.

commit cee9e8b8d814bc0aaefacaf9bdc81d5ca2f2876b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 1 15:47:28 2015 +0200

    Added Interfragmenter::findLargestCutoff() to find largest Rcut not causing additional inter-fragments.
    
    - so far, the function is only used in FragmentationAction by merely printing
      the distance.

commit b1c5f46c2e8356c3a5cb7319f77fe3e21793f787
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 1 15:46:05 2015 +0200

    Interfragmenter now combines two fragments up to (in sum) till MaxOrder.
    
    - before only fragments of each MaxOrder were allowed, now the sum of their
      bond order must not exceed maxOrder, i.e. MaxOrder of 4 means 1+1, 1+2,
      1+3, 2+2, 3+1, 2+1, 1+1 (with order of left and right fragment that are
      joined).

commit 0d90534c2cfcca7121d5161e6f235225bdb4c0df
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 1 10:31:54 2015 +0200

    Exracted several functions out of Interfragmenter::operator().
    
    - extracted Interfragmenter::getAtomKeysetMap(), ::getNeighborsOutsideMolecule(),
      ::getAtomSpecificKeySetMap(), ::combineFragments().
    - this is preparatory for enhancing the Interfragmenter to automatically
      ascertaining a certain "distance" between fragments for long-range
      interactions. That is, we may afterwards smear out nuclear and electronic
      charge distributions up to said distance without them overlapping outside
      of a present fragments (i.e. without capturing their short-range interactions
      elsewhere).

commit 7537d191a569f0b72f4ef6db9b9ae70d575a463f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 16 17:05:28 2015 +0100

    Removing setting net force to zero and setting hasForce to true.

commit 00d815ca595052983db7c34a5f62e31c775c680e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Feb 14 12:58:32 2015 +0100

    FIX: Need to divide by global number of particles, when summing later, in ExportSolution.

commit 6e73f5af95ffb4eb1a979d776df10f17828e74f9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:01:51 2014 +0200

    Added debugging changes to InterfaceVMGJob on force summation.

commit ff347fc31ed5cd23e7ad30c79dd005ca9145acb2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Feb 7 12:21:09 2015 +0100

    Added gathering of full and longrange forces into extra file.
    
    - added new structs to VMGDataFusedMap for summation.
    - tempcommit: we do not have the full index set available, hence it just
      accumulated all indices from all fragments into a sorted set and use this in
      lieu of the full index set. We need to check how the full solution is
      constructed and how indices to the particles and their force vectors can
      be assigned.
    - extended printFullSolution() by another table with short- and long-range
      forces.

commit 20bb3b83b5704876159d8aeede5c88f78cb27559
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:00:30 2014 +0200

    MPQCData now also uses FragmentForces (instead of typedef forcevector).
    
    - required small changes to MPQCCommandJob due to changed typedef.
    - we need to maintain the old code which used vector of forces. Therefore,
      the serialization version of MPQCData is increased and a simple conversion
      routine added.

commit 94db134a7b8bcdb17a2134fe1c6ca1aed4aded49
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 23:56:32 2014 +0200

    Again changes to obtain correct longrange forces, also forces are optional.
    
    - renamed particle_forces -> forces to make it consistent with MPQCData_Fused.
    - MPQCData_Fused and VMGData_Fused are structs and no longer namespace as the
      latter cannot serve as template arguments.
    - split off forces in VMGData into VMGDataForceMap_t and VMGDataForceVector_t.
    - changed ConvertMPQCDataToForceMap() into template function
      ConvertDataToForceMap(), working also on VMGDataForceMap_t.
    - this required changes in FragmentationShortRangeResults.
    - FragmentationLongRangeResults now also converts the longrange forces
      correctly.
    - AnalyseFragmentResults now prints also a ..VMGForces.dat file.
    - VMGData's forces are now optional to some degree and analysis chain can deal
      with it.
    - introducing forces we must still maintain working code when results without
      forces are calculated (e.g. as in the regression tests). Hence, a boolean
      im VMGData and FragmentationLongRangeResults states whether forces have been
      found or not and whether these should be summed up or not subsequently.

commit 14a618bda4c5471ea8d26d9429a8c964bd366dff
Merge: b19f280 b61bd5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 13 22:10:12 2015 +0200

    Merge branch 'Fix_debianpackage' into Candidate_v1.5.2

commit b19f2801b7152275a338f8cc95c051ccd1679bb7
Merge: 18f47f8 24f4251
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 13 22:10:00 2015 +0200

    Merge branch 'Fix_ActionQueue_lastchangedaction' into Candidate_v1.5.2

commit 18f47f88da033fc8b97a339b874684f5aba29199
Merge: 0a3449a dace6c7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 13 22:09:38 2015 +0200

    Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.2

commit 0a3449a7a998a2d08cf2b499e980ab657da627b8
Merge: dcff593 2f429ef
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 13 22:09:22 2015 +0200

    Merge branch 'Better_HBondDistances' into Candidate_v1.5.2

commit dcff593de06c56b6b49d074d77955a90c552aaa2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 31 14:38:50 2015 +0200

    Implemented more efficient per-molecule bounding box information.
    
    - molecule now has internal bimaps to know the extent of itself in a cheap way,
      right map needs to be multiset_of to allow for non-unique values.
    - moved BoundingBoxInfo from GLMolObject to molecule.
    - is itself a Cacheable and is requested from GLMoleculeObject_molecule on new
      channel BoundingBoxChanged.
    - Cacheable listens to AtomInserted, AtomRemoved, and AtomMoved.
    - in molecule::changeAtomId() we also change BoundingBoxSweepingAxis entry.

commit a06378771ff430b3ce4652d680ae761a08426668
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 31 14:38:30 2015 +0200

    FIX: Removed double coding in molecule::erase().

commit 59e799680d2829d1437a7c22cb6820332ca100a5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 13 16:33:52 2015 +0200

    FIX: World needs to first destroy the atom, then release its ids.

commit ceaab1dbd47046505deba359f3a96512689de872
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 29 09:40:52 2015 +0200

    AddAtom now adds a molecule (atom always associated with a molecule).
    
    - also by default, constructs a new molecule if none has been selected.
    - we missed changing the atom id on redo (new ones have different ids) and
      especially now telling the associated molecule about it. This is changed
      with a new molecule::changeAtomId().

commit b61bd5e8f51d73a916f0e0a2fcd4dcadcf84dfd8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 2 23:10:12 2015 +0200

    Fixed levmar m4 to use pkgconfig and locate.
    
    - we don't need to give with-levmar which allows debuild to make use of the
      installed package.

commit 6227207a85bc7078c5be7985f12def5bac3f8287
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 2 23:09:53 2015 +0200

    Added all required libboost.. to Build-depends.

commit 3c6b4067162cb45d4e7ac87de102c3c8683d0a5b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 28 12:41:00 2015 +0200

    Changed debian files to heber at molecuilder.com and changed boost dep.
    
    - we now just depend on libboost-dev (i.e. on all).

commit 2f429ef69adf29a1bf0267338e9cecd1fb5b238c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 22 20:02:47 2015 +0200

    Elements are now parsed as string (and tried for being int).
    
    - this allows to parse both "He" and "2", i.e. both symbol and atomic number.
    - this works for both command-line and Python.

commit 3b1c369fabf5039957cb70e0059346c668d0eebf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 11 08:40:03 2015 +0200

    Entered HBondDistance results from VSpeShape into elements_db.
    
    - we now have single bond distances for all elements from 1 to 37. They are
      mostly consistent with the old values (but some are not, e.g. for element no
      20, but they look like copied).

commit c85c2e7c1a8f696987bf232998d8eef09d386b99
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 11 03:33:54 2015 +0200

    FIX: Element's HBondDistance and HBondAngle were not initialized as -1.
    
    - this causes faulty behavior with saturate-atoms (e.g. Li) which showed the bug.
    - TESTFIX: ElementUnitTest adapted to new default behavior.

commit 4f8079f804337514271581f8a67c750b656f2fbb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 10 17:16:57 2015 +0200

    Added Hbonddistance and -angle for sodium (Na).

commit e3c4c532b457c1d83d8ac94e74300e037b757ace
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 10 16:41:24 2015 +0200

    MpqcParser additionally allows to save optimization jobs.
    
    - this is enabled via a new flag "jobtype" that can be either Default or
      Optimization.
    - also storing "checkpoint = no" per default for all mpqc input files. This is
      a safety measures such that no old checkpoint files are used that reside in
      the same folder accidentally. This is especially important for fragment
      files.
    - TESTFIX: changed all regression tests comparing against .in files, added
      new checkpoint statement.
    - TESTFIX: changed unit test ParserMpqcUnitTest in the same manner.

commit 6c30ab3e28b74461e5739b1fae84da32b57c8642
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 10 16:19:41 2015 +0200

    Assertion in SaturateBond now states element.

commit d79ca1b812618b68d1781fb9ef48651c790f66f0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 30 19:54:29 2015 +0200

    FIX: SaturateAction would use double instead of single hydrogen bond length.

commit 2a7dbe1527726bfd2bc8d6793a86c59deefc3fdf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 8 10:17:13 2015 +0200

    FIX: Help on SetBoundaryConditionsAction did not have capitalized condition name.

commit 83a425eb7c3e26118a81096a43c79ffe877b2113
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 12:49:02 2014 +0200

    Split off sampled_potential im VMGDataMap_t into separate fusion container.
    
    - this should correct the output in ..._VMGEnergy.dat

commit ce98747dfef7546f47996405283750bc34c9ad5d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:30:19 2014 +0100

    Added extraction of long-range forces from VMGData's array f.

commit d200ae2e4a4f8002d6ef527fd7bfa418be477b9c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:31:42 2014 +0100

    Added new SetValues FragmentForces.
    
    - struct is particle_forces used in fusion maps and vectors.

commit 057c8a49f208862ececbcb5c1adeaf0566d89313
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Feb 7 12:18:59 2015 +0100

    FIX: When there's just a single fragment, don't remove the fullsolution.
    
    - this usually causes some assert to hit when we test the long-range
      calculation on a single water molecule where there's only a single fragment
      and it conincides with the full molecule. Hence, the full solution
      calculation does not cause an extra fragment job.

commit 9593d16ae241f82c256733f785601e2e0cfb9b29
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 19:29:19 2014 +0200

    FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob.
    
    - note that so far domains needs to be cubic.

commit c20839bcb1af30decfbda10a56579a6b43c683be
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:54:37 2014 +0200

    FIX: Shared libraries's Makefile.am rules are now consistent.
    
    - pkgconfig is just given once (in src/Makefile.am).
    - all have version information, including now pyMoleCuilder.so.

commit 24f425178ef9717a191dfb42f15da6fc45bbc899
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit dace6c77620134a6d8c643e895a7d94794d97f13
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 4 14:26:53 2015 +0200

    FIX: tests/GuiChecks/atlocal lacked valgrind variable.
    
    - note that running molecuilder through valgrind currently produces loads of
      error messages all connected to the Qt and/or python parts and have in the
      vast majority nothing to do with molecuilder. We will use our own memory
      debugger until suitable suppression files can be found. Until that not
      sensible debugging of memory leaks is possible in the GUI part of the code.

commit 08d9df7e636ea0df65e73df162455c8f47deb448
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 2 11:59:44 2015 +0200

    FIX: Rename codepatterns -> libcodepatterns.
    
    - updated makeDebianPackage.sh to compile with multiple cores.

commit ba353982fb33936c0b6e4c92a14dba221dc08c56
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 29 13:47:45 2015 +0200

    Package CodePatterns is now called libcodepatterns.
    
    - updated m4 file.
    - also updated .pc files.

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