This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "". The branch, GUIStates_using_ObservedValue has been created at f4dee7e64136fb00c69ffb78887757d27f7e6506 (commit) - Log ----------------------------------------------------------------- commit f4dee7e64136fb00c69ffb78887757d27f7e6506 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sat Jul 25 15:06:15 2015 +0200 Revert "TEMP: Removed QtLogBox for the moment." This reverts commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39. commit eb45df7aec04234f11a15950d18e59516b7ce4c2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 23:54:14 2015 +0200 TESTFIX: Marked molecule translation guicheck tests as XFAIL. - so far, we cannot use a MakroAction as a python function except if not arguments are required. Hence, for the moment we mark it as XFAIL. - The problem is with the boost::python::def function. We need to fill its arguments during compile-time but that would require some weird preprocessor magic going through all Actions contained in the MakroAction's sequence. commit d64e8627471715a028543ed12651ae69d43b0853 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 22:47:41 2015 +0200 FIX: GLMoleculeObject_bond had both flipped ids and the side. - in essence, both do the same thing. We removed all switches that check the sides as flipped ids are actually nice and look good in the observerLog. We keep the side variable as it might come handy for checking which one we are. commit 2692644e10e1ccab3040ac8d3fb9b02b19e1d8d4 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 22:22:53 2015 +0200 FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more. commit 168f09c04553c61e675bd054a387752cb05b8e37 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Jul 20 11:16:27 2015 +0200 FIX: Fixing display of shapes in GLWorldView. - we propagate shape name via S/S system such that we may lookup the name in ShapeRegistry and do not have to rely on probably already deallocated lastchanged() shape. This affects ShapeAdded() and ShapeRemoved(). - GLMoleculeObject_shape now copies the shape, ensuring that its present while its surface is tesselated. commit be045266fe862bc3616debab8493f5cbcc8c6df3 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 15:47:57 2015 +0200 GLWorldScene lacked assert of Walker in atomClicked(). commit 9689958e7cf83fc56bd3ce101b4e2377812bbdcc Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 15:47:19 2015 +0200 Asserted that GLMoleculeObject_molecule::update() is never called. commit 4999cc1bdc8e0dc998b84667d9ac76e074740559 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 15:46:41 2015 +0200 AddAtomBonds() now uses just id not ptr as param. commit bb3c6395fc5644893150017d8d77267f10f341ce Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 15:46:02 2015 +0200 Avoided use of getId() on molecules and atoms in Qt code where possible. - it is ok if we are inside O/O functions or functions called from these functions. commit fc77fcc5b4e421bc290d5668e79bc06aa0d0a195 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 15:29:37 2015 +0200 GLMoleculeObject_molecule does not use getAtomCount() anymore. - this removes any usage of getAtomCount() apart from ObservedValue's. commit 93b577e41a565c39eb678b2f8e81493bdd45348f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 15:25:40 2015 +0200 GLMoleculeObject_molecule also has ObservedValue for name. - this removes any (uncached) molecule::getName() from Qt code part. commit adf47b24e5cc5141e099c87dc99b5dd4b442adb5 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 14:01:14 2015 +0200 FIX: Setting molecule's name via QtMoleculeList item is again possible. - this is similar to checkForVisibilityChange(), only now for the name. - we required four Actions, i.e. this cannot be undone in a single step but needs four. However, right now it is not easily possible to construct MakroActions from inside the code at compile-time as we do not have access to modify parameters via their tokens. - using constructed MakroAction in QtMoleculeList for name change. commit 4020599c23ade7363303a5945af85be91ef1a8db Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 13:35:26 2015 +0200 Fixed formula usage in Qt part of code. - formula of a molecule is only access through ObservedValue or directly within the World's O/O system. - Molecule may disappear before selection event. - Atoms may disappear before selection event. commit 1dfe95e16fd32fa72b2a1e71a4cc8bd14618b18e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 09:08:38 2015 +0200 QtMainWindow uses QtSelectionChangedAgent. - QtMoleculeListView and GLWorldView receive its signals. The latter passes it on to GLWorldScene. - QtMoleculeList has new MoleculeIdToIndex to allow QtMoleculeListView to (un)select specific rows on a given index. - GLWorldScene passes atom and molecule selection to GLMoleculeObject_molecule. - GLMoleculeObject_molecule passes atom selection to respective GLMoleculeObject_atom. commit 074baadc91e211ccd41147af6abf799b71fc3627 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 08:36:38 2015 +0200 Added QtSelectionChangedAgent to transform O/O to S/S system. - also this will be far more effective, as e.g. not all GLMoleculeOBject_molecule will receive SelectionChanged from World if just a single molecule has been selected. - Atom might not yet have a molecule, i.e. it is not drawn yet. We do nothing then. - recieveNotification allows for vanished atom (due to removal). We do nothing then. commit 09e0ca3e6e28262e077f40053ebf67bab3e4796f Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 08:30:51 2015 +0200 QtMoleculeItem_.. now shout when they receive subjectKilled(). - this way we do not have this double system of both QtMoleculeList (in a lazy fashion) and each QtMoleculeList listens for moleculeRemoved (one through the Observer channel, the other through subjectKilled()). - we simply count the number of QtMoleculeItems that received subjectKilled() and if max is reached, the row is removed. - to prevent molecule id clash, insertion (of same id) after removal is ok. This works cause we first remove and then insert new item. Hence, having the same id is possible. commit 4762b3173f12c0642c489500083fad1589bf2072 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Jul 16 10:29:09 2015 +0200 FIX: Fixing "pure virtual function called" in QtMoleculeItem. - as a matter of fact this should not be a problem: Inside QtMoleculeItem's dstor body while signing off from the channels, it is no problem to receive a notification for a channel we have not signed off yet. The vtable has not been touched with respect to QtMoleculeItem. I really do not understand this issue. I have tried to reproduce it with a few mock classes that have the very same inheritance pattern and used locks to force the same case of a virtual function being called while inside the dstor's body but it does not reproduce the error. - the same holds for the cstor and again the vtable is created before the code pointer enters the cstor body, hence it should be no problem ... - the solution is to signOn..() and signOff..() on the highest level, i.e. on the most derived classes. This causes some code duplication but at least it works. commit 245e9692a44164808c463d60ad0de5a7c2392611 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Jul 16 01:26:09 2015 +0200 World now first releases id and then destroys the atom/molecule. - this prevents any access to atoms/molecules in the phase of destruction. commit 5c981e3c50a9ce1f9f4718105c813b8ca4c67fc9 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Jul 16 01:25:22 2015 +0200 Qt4 instance use new lastChanged..Id() in place of lastChanged(). commit 560fde03092bed821426b2947d5ed75433a9f5ce Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Jul 16 01:23:30 2015 +0200 Added lastChanged..Id() to both World and molecule. commit 74eca4ad3c549f66044ae4c6e9f516b06b657004 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Jul 15 17:22:04 2015 +0200 GLWorldView no longer listens to WorldTime::TimeChanged. - molecules are re-created when the time changes anyway so the world view is informed about the change. - removed all commented-out lines. commit f3c5c4c66787aa0d57c075b774bd31837f92ec1b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Jul 15 16:01:41 2015 +0200 GLWorldView does not emit changed() on each general update() from the World and others. commit fe3a8edd8283948b1fc0ef245734b7fcb1bfa24d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Jul 15 15:56:58 2015 +0200 DOCU: Updated documentation on Qt Gui construct. commit 7ec5b58a4b1f90c652d45fd9a7e5b880d0128d69 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Jul 14 15:55:47 2015 +0200 Fixing QtMoleculeList with list containing only formulas and ids. - COLUMNTYPE now belongs to QtMoleculeItem not QtMoleculeItemFactory. - callback function in QtMoleculeItem signature changed to molid and column. - QtMoleculeItem::getType() for obtaining the type to be used as argument in the callback. commit 16a82a5ef43facec7c668ec74e9046afcda7cf01 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Jul 7 03:10:10 2015 +0200 QtMoleculeList::informDirtyState() does not need to lock refill_mutex anymore. - we simply write the QtMoleculeItem to the ToBeMoved list and convert it to the very first item in the row in updateItemStates(). commit 4653d0ae75870324e5370916e54cb8cb0cef23a6 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Jul 7 03:08:58 2015 +0200 Fixing QtElementList::updateElement(). commit b1edc5e445b076a4f6a98cc2ad6351fae695782e Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Jul 20 10:35:41 2015 +0200 GLWorldScene propagates changed mol id to GLMoleculeObject_molecule. - GLWorldScene must emit MoleculeRemoved on last subjectKlled(). - GLWorldScene has internal RemovalMolecule in case moleculeRemoved comes prior to moleculeInserted. commit 42755eeaab85ae4e85390719b64ae360d7adcd98 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit 7a7d0aed5391ad7c8f1eda65f06dfd6e8355609c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jun 21 06:49:13 2015 +0200 QtMoleculeItem_... use ObservedValue for internally representing atom's state. - this affects atomcount, formula, and name. visibility depends on clicked state and occurrence is changed elsewhere. commit 24c9a0b1a01c01cea59c2ef164eea1464f05c885 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit cc2dc6d9e9e20e77513818ccde1e884d51353f1b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Jun 19 19:37:50 2015 +0200 GLMoleculeObject_atom uses ObservedValue for internally representing atom's state. - we use internal owner as ref to Observable. commit d98069265ba6fa55594b9b574ea8d18216cd89aa Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit 92be0d3e0a4164d2d47d5f705fc955cf12f899b9 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 5 09:55:15 2015 +0200 Using static Observable::..NotificationsChannel() functions. - requiring now CodePatterns 1.3.0 due to ObservedValue. - also we purge the GlobalObservablesInfo in cleanUp(). commit c66ae6684084ff864820af9b907d9f3b9725530d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 18:36:06 2015 +0200 TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in save-adjacency regression test. - GuiChecks sees a different (but still valid) ordering in the .adj file in the save-adjacency regression test. commit f7054cab5c6c0b7c73d7b4866501383e989b50da Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 18:13:44 2015 +0200 TESTFIX: selection molecule by name had escaped ticks. - also changed GuiCheck tests. commit 80f678157992ab9328be5ba384216ae6e1548684 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 12:03:43 2015 +0200 FIX: Added Parameters Value_Elements to correctly set vector of elements from string. - this fixes that fit-potential action is not correctly called from python scripts. There, we require correct setter of a value from a given string. As all arguments to a python command must be given as single string, even if it is a vector of arguments, we must correctly decode this string again. commit c569220c375bbffdf838cc2cfd11de122bf57a86 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Jul 8 12:33:49 2015 +0200 TESTFIX: regression test DepthFirstSearch had extra linebreak. commit 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Jul 8 08:47:52 2015 +0200 TESTFIX: atom selection regression tests with shapes were very noisy and hence very slow. commit 7a0456949e5c8efe51fc75d2a5902483c296feec Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Jul 6 15:07:00 2015 +0200 TESTFIX: regression test SubgraphDissection Redo was broken. - also changed derived GuiChecks test. commit 42b40a4b4a9210b1ed60a0be93acd12541dedde9 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Jun 19 13:45:49 2015 +0200 Added TriangleMatcher to safely compare tesselation .dat files. - is used in tests/regression Tesselations, tests/Tesselations, and has its own regression test, too. Also added tests/GuiChecks. - added trianglematcher to testsuite dependencies. commit a82f61a466e15715e16f9470a56c3bdadfcb3895 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 14:39:16 2015 +0200 Added Action::setOptionValue() which allows setting the option via a string. - this is preparatory for allowing the creation of MakroActions inside the code. We need to set the options without going through dialogs in some way or another and without being completely inside the Actions as is the case for the COMMAND variants and the python function calls. commit 143263bb92532b8d3e50535a2c7cfae698a6ab6d Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 08:15:39 2015 +0200 Added getSelected..Ids() for both atoms and molecules. - added static function getKey() to _take in Helpers. commit fe0ddfc870329d8adcaf7269129b4690ddd98db4 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 22:58:57 2015 +0200 FIX: atom_atominfo lacked some notifies or had them wrong. - ElementChanged only when element actually changes it not helpful (QtElementList has then no chance of detecting new atoms with default element of hydrogen). - TrajectoryChanged was signalled only when current timestep was added or removed, rather we signal always and assert that we do not remove or append the current time step. commit f5452477d87da2369a118585276d5b6793a46480 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jun 21 15:34:40 2015 +0200 FIX: Molecule has new signal IndexChanged. - this has been overlooked so far, index may be changed similarly as for atoms. commit c6719db9d555d7c3f1b43c5cd90b1ccc2a8df1c8 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jun 21 06:45:30 2015 +0200 FIX: atom_bondedparticle signatures changed to more const versions. - added getBond() for obtaining bond in const manner. commit df3f2f34f6c9dbddae6f42d32b7a644c3b756eb8 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 20:29:39 2015 +0200 Group item with atom count of 0 is confusing in QtMoleculeList, creating with empty string. commit a963cf91fe5fac81f5a6c9c3e2c5d8100868fea3 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Jul 19 12:03:05 2015 +0200 executePythonScriptFile() calls executePythonScript() now. commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Jul 20 00:21:57 2015 +0200 FIX: QTUIFactory's test-single was not working right. ----------------------------------------------------------------------- hooks/post-receive --