From git at ins.uni-bonn.de Wed Jul 8 08:54:02 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:54:02 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.11 deleted. v1.4.10-47-g2fc697b Message-ID: <20150708065402.9BABD5FD6E@saturn.ins.uni-bonn.de> 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, Candidate_v1.4.11 has been deleted was 2fc697b743f39b710d3866f7ce2c17542470e39f - Log ----------------------------------------------------------------- 2fc697b743f39b710d3866f7ce2c17542470e39f Set version to 1.4.11. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 8 08:55:13 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:55:13 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] annotated tag v1.4.11 created. v1.4.11 Message-ID: <20150708065513.4B72B5FD6E@saturn.ins.uni-bonn.de> 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 annotated tag, v1.4.11 has been created at 493beb6da4a6da7c28cace5bb7c7b8452194a130 (tag) tagging 2fc697b743f39b710d3866f7ce2c17542470e39f (commit) replaces v1.4.10 tagged by Frederik Heber on Wed Jul 8 08:31:58 2015 +0200 - Log ----------------------------------------------------------------- Several smaller GUI fixes (but this is just the start of it) and other nice-to-haves SphericalPointDistribution allows saturation of arbitrary elements with hydrogen atoms. Several regression test fixes. Initial version of a GUI testsuite (python script + GUI). This version contains the following branches: 2fc697b Candidate_v1.4.11 (distcheck fixes and setting version) 08d042d MolecuilderGuiTestSuite (--test and --test-single launch python scripts with active GUI, adding internal DryRun actions) 19dfdf7 GUI_niceties (enhancing QtInfoBox, ...) 3a4be0d SeveralRegressionTestFixes (Fixes within the testsuite statements) b9b49e7 SphericalPointDistribution (initially planned for the final solution to hydrogen saturation in the fragmentation scheme, it allows now to simply add hydrogens to any atom in the system and saturating its orbitals) f47efd4 SeveralGUIFixes (Lots of small fixes that came up when using the GUI) Frederik Heber (47): FIX: Action..::outputAsPython now accesses parameters via getUnvalidated(). FIX: RotateAroundSelf converted rotation angle to rad in params. FIX: UndoRedoHelpers' AddBondsFromBondInfo would add bonds doubly. Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId(). Undoing atom/molecule removal will also recreate bonds. FIX: [push/pop][Atom/Molecule]Selection would store ptrs instead of ids. FIX: All MakroActions now have prototype_actions and copy from that. Added correct-bonddegree to MolDyn and StructOpt Actions. Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect. FIX: ActionSequence now checks whether an Action in the sequence fails. FIX: FragmentationAutomationAction checks FragmentControllers' exitflags. FIX: MPQCCommandFragmentController failed to add jobs due to false return value type. FIX: QDebugStream is now protected against multiple writes to log window. FIX: MPQCData::DoValenceOnly was wrongly initialized. TESTFIX: Output for target "extracheck" in logs is not helpful if just the log is sent back. FIX: Bond cylinders were wrongly scaled and too long with degree larger than one. Added matchSphericalPointDistributions() to SphericalPointDistribution. Added unit tests for SphericalPointDistribution. Moved all code from header of SphericalPointDistribution into cpp module. Trimmed down SphericalPointDistribution to what is needed at the moment. Added SaturateAction that uses SphericalPointDistribution. Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms. createMoleculeMesh now checks that minradius is at least the minimum bond length in the molecule. QtInfoBox shows Atom's position components separately and molecule's center. FIX: QtMoleculeList hiccup'ed on update-molecules for two water molecules. Increased timer interval in QtStatusBar to 4secs. FIX: Setting window title in QtMainWindow. FIX: Fastparsing regression test contained one broken line. FIX: VerboseAction would store invalid undostate (just success). FIX: double inclusion protection used already used name. Split executePythonScript into file and string script option. FIX: Removed specific queries for RandomNumberDistribution_Parameters. Added "--test"-mode to UI switch in builder_init. Command-line arguments are passed to QApplication inside QtUIFactory. Added testsuite "GuiChecks" with extra target guicheck. Added GuiCheck "AddAtoms". Added DryRun and NoDryRun actions. Added script file to generate guichecks testsuite from regression tests. Added all new guichecks regression tests generated from createGuiChecks.sh script. Added ParameterPair (i.e. "key = value;") to allow other string output. Replaced all std::string by ParameterPair where used as ("key = value;") tuples. Replaced Query.. class and query..() function declarations in Dialog.. by boost preprocessor magic. Added "--testsingle" switch for line-by-line execution. Merge branch 'GUI_niceties' into Candidate_v1.4.11 FIX: QtUIFactory used executePythonScript without HAVE_PYTHON brackets. FIX: ActionQueue would not set LastActionOk to false on general exception. Set version to 1.4.11. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 8 08:55:20 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:55:20 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch stable deleted. v1.4.10 Message-ID: <20150708065520.0602A5FD6E@saturn.ins.uni-bonn.de> 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, stable has been deleted was 2e7afe95e7fc92ca90ef771dbb8089a436d2189a - Log ----------------------------------------------------------------- 2e7afe95e7fc92ca90ef771dbb8089a436d2189a Set version to 1.4.10. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 8 08:55:22 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:55:22 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch stable created. v1.4.11 Message-ID: <20150708065522.AB26A5FD6E@saturn.ins.uni-bonn.de> 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, stable has been created at 2fc697b743f39b710d3866f7ce2c17542470e39f (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 8 08:55:37 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:55:37 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch MolecuilderGuiTestSuite deleted. v1.4.10-39-g08d042d Message-ID: <20150708065537.EE7295FD6E@saturn.ins.uni-bonn.de> 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, MolecuilderGuiTestSuite has been deleted was 08d042d999587b9169fbb5763d93a65241a1cf4f - Log ----------------------------------------------------------------- 08d042d999587b9169fbb5763d93a65241a1cf4f Added "--testsingle" switch for line-by-line execution. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 8 08:58:18 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:58:18 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch DebianPackaging deleted. v1.4.10-73-g391923a Message-ID: <20150708065818.1E1355FD6E@saturn.ins.uni-bonn.de> 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, DebianPackaging has been deleted was 391923ab6c70fce7fc420886301c9b8a1bc0be4d - Log ----------------------------------------------------------------- 391923ab6c70fce7fc420886301c9b8a1bc0be4d Added script for creating debian package. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 8 08:58:22 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 8 Jul 2015 08:58:22 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch DebianPackaging created. v1.4.11-5-g804b7fc Message-ID: <20150708065822.28B6D5FD6E@saturn.ins.uni-bonn.de> 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, DebianPackaging has been created at 804b7fc9d8004fcfadf39477d9483baeb8cbc4be (commit) - Log ----------------------------------------------------------------- commit 804b7fc9d8004fcfadf39477d9483baeb8cbc4be Author: Frederik Heber Date: Sat May 23 21:04:44 2015 +0200 Added script for creating debian package. commit fb9681e0d8857408361736f327c00b3ab40d3689 Author: Frederik Heber Date: Sat May 23 11:26:47 2015 +0200 Added debian/.. files for debian packaging. - added all dependencies (without JobMarket, QtGui, QWT, or vmg). commit ae592e40a6e82e0c204b29f3f94b15871fe73e46 Author: Frederik Heber Date: Sat May 23 20:32:37 2015 +0200 FIX: bash_completion was accidentally removed by clean target. - also Python/boxmaker was not contained in EXTRA_DIST. commit 7e8a27bd8d3860f24450c09bb031bf8cbb4a582f Author: Frederik Heber Date: Sat May 23 20:32:01 2015 +0200 DOCU: Described workaround for missing pyconfig.h. commit eb27601ec7e5eaa340e537daf44d5077aad8b97d Author: Frederik Heber Date: Sat May 23 16:23:14 2015 +0200 FIX: AllPotentialHealder.hpp not excluded from CodeCheck config_h. - this only causes an error when not doing an out-of-source bild (which debuild does and that's why it came up). ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:02:26 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:02:26 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch SeparatingOutQtThreads deleted. v1.4.11-70-g935c985 Message-ID: <20150725130226.F32685FD6E@saturn.ins.uni-bonn.de> 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, SeparatingOutQtThreads has been deleted was 935c9855a319b377fe6bcf247e2c9430fc26b545 - Log ----------------------------------------------------------------- 935c9855a319b377fe6bcf247e2c9430fc26b545 tempcommit: trianglematcher also used in GuiChecks. Merge with ... ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:02:35 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:02:35 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue deleted. v1.4.11-87-ga8e27aa Message-ID: <20150725130235.1F2A95FD6E@saturn.ins.uni-bonn.de> 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 deleted was a8e27aa65ba2fcf21bb580942f710348a3472e86 - Log ----------------------------------------------------------------- a8e27aa65ba2fcf21bb580942f710348a3472e86 tempcommit: Fix to _molecule. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:14:11 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:14:11 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch SphericalPointDistribution deleted. v1.4.9-63-gb1da407 Message-ID: <20150725131411.8D0AA5FD6E@saturn.ins.uni-bonn.de> 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, SphericalPointDistribution has been deleted was b1da40790a94dda83c5afbc4a9e1fd91285b21b8 - Log ----------------------------------------------------------------- b1da40790a94dda83c5afbc4a9e1fd91285b21b8 Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:14:36 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:14:36 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch SeveralGUIFixes deleted. v1.4.9-53-g8e07caa Message-ID: <20150725131436.04D195FD6E@saturn.ins.uni-bonn.de> 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, SeveralGUIFixes has been deleted was 8e07caa814fbc579f0cb407b840da546eb6d2025 - Log ----------------------------------------------------------------- 8e07caa814fbc579f0cb407b840da546eb6d2025 FIX: Bond cylinders were wrongly scaled and too long with degree larger than one. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:15:11 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:15:11 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch AddingConstDescriptors deleted. v1.4.11-53-g3a7fbdb Message-ID: <20150725131511.22FAC5FD6E@saturn.ins.uni-bonn.de> 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, AddingConstDescriptors has been deleted was 3a7fbdb3980327cf8c58023011fc82e04ec2ff45 - Log ----------------------------------------------------------------- 3a7fbdb3980327cf8c58023011fc82e04ec2ff45 FIX: GLWorldView was signed in to atomInserted and atomRemoved without any need. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:15:24 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:15:24 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch Fixing_MolecuilderGui deleted. v1.4.11-16-g8cd4341 Message-ID: <20150725131524.16E645FD6E@saturn.ins.uni-bonn.de> 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, Fixing_MolecuilderGui has been deleted was 8cd434159764699e9aa7b69302b9835339eee8f4 - Log ----------------------------------------------------------------- 8cd434159764699e9aa7b69302b9835339eee8f4 tempcommit: Attempt to replace QtElementList::refill() by faster system. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Sat Jul 25 15:16:11 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Sat, 25 Jul 2015 15:16:11 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUI_smallerchanges deleted. v1.4.8-22-g107bfd9 Message-ID: <20150725131611.902635FD6E@saturn.ins.uni-bonn.de> 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, GUI_smallerchanges has been deleted was 107bfd9a3f982894a7922552138617bab4d117b7 - Log ----------------------------------------------------------------- 107bfd9a3f982894a7922552138617bab4d117b7 Increased timer interval in QtStatusBar to 4secs. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Mon Jul 27 09:03:21 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Mon, 27 Jul 2015 09:03:21 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch AddingConstDescriptors created. v1.4.11-44-g9ad4d61 Message-ID: <20150727070321.940A45FD6E@saturn.ins.uni-bonn.de> 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, AddingConstDescriptors has been created at 9ad4d612899bb1547d6400f43c8330480c78d103 (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Mon Jul 27 09:03:21 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Mon, 27 Jul 2015 09:03:21 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue created. v1.4.11-107-gb47abff Message-ID: <20150727070321.A1F645FD6E@saturn.ins.uni-bonn.de> 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 b47abff064ca6c1c30e67de797d8e0caeba61813 (commit) - Log ----------------------------------------------------------------- commit b47abff064ca6c1c30e67de797d8e0caeba61813 Author: Frederik Heber Date: Sat Jul 25 15:06:15 2015 +0200 Revert "TEMP: Removed QtLogBox for the moment." This reverts commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39. commit 00d3632c7fa7a8799e6b6a50cc1e256654299bf3 Author: Frederik Heber 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 b33dcdfdaded609fa04eaa2495e51bfe4300e248 Author: Frederik Heber 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 ea091658023c2737b75aec0cd24a8c7ff3916755 Author: Frederik Heber Date: Sun Jul 19 22:22:53 2015 +0200 FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more. commit 19bc4cc03a49f716b1d846fb4a5ecee5b8ec7672 Author: Frederik Heber 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 b2bc49200adaf0e61c05f37adc4612cf71ef0b58 Author: Frederik Heber Date: Sun Jul 19 15:47:57 2015 +0200 GLWorldScene lacked assert of Walker in atomClicked(). commit a7dd6fdf92d6b53191e61bb02351aa4f37efa8d3 Author: Frederik Heber Date: Sun Jul 19 15:47:19 2015 +0200 Asserted that GLMoleculeObject_molecule::update() is never called. commit 82b2c3f0788ef37d5452d1eca1bb1fc2bf9e2b9f Author: Frederik Heber Date: Sun Jul 19 15:46:41 2015 +0200 AddAtomBonds() now uses just id not ptr as param. commit b2b58e8795806658b1826b946c4e486527b25d96 Author: Frederik Heber 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 6bad8aaf6f9186b8b2c88f7450e20bb4a7b9c2ac Author: Frederik Heber 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 834577c49f896c34887ca40809d96522a6397349 Author: Frederik Heber 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 8d170f3d282ef6c9fa98795214be822adcac56d0 Author: Frederik Heber 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 6e280b0a98ef844794c6cdf6d544046e2e500a7b Author: Frederik Heber 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 35cb3c8d7d8f15c85ce65041e6001885fce892e4 Author: Frederik Heber 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 28533e9a1336c37b970604e1e371ea30c467a9e4 Author: Frederik Heber 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 bd1a4c8203cca6b6b5b6722ed7adfe5afdde6278 Author: Frederik Heber 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 a62da4bf1e209ff5ed585d779e7879ad287efa0b Author: Frederik Heber 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 0136d52ac341be8c1e24ea26b09af36ad982bd38 Author: Frederik Heber 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 54a24aa3cfb8c174f59d9572566cde5a4c000685 Author: Frederik Heber Date: Thu Jul 16 01:25:22 2015 +0200 Qt4 instance use new lastChanged..Id() in place of lastChanged(). commit 17cd32b0c3ef5c75207ea4a55f30a481df495f6e Author: Frederik Heber Date: Thu Jul 16 01:23:30 2015 +0200 Added lastChanged..Id() to both World and molecule. commit 653478cd9fe3579c656f55a639edcf783d30d25e Author: Frederik Heber 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 bd6a00bb272bc4854106d2d7fad5ec8861de0b45 Author: Frederik Heber Date: Wed Jul 15 16:01:41 2015 +0200 GLWorldView does not emit changed() on each general update() from the World and others. commit 8cd7c8630c85118f5a86e7bfafc16d3139011a3e Author: Frederik Heber Date: Wed Jul 15 15:56:58 2015 +0200 DOCU: Updated documentation on Qt Gui construct. commit 40b96def4ffe2b0be3a0b2666f57839ab8f07fe9 Author: Frederik Heber 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 c8d26b410eb40966f4de6b0b656a8f86fdfcebcc Author: Frederik Heber Date: Fri Jul 10 12:54:51 2015 +0200 Using static Observable::..NotificationsChannel() functions. commit 6f77b02791e569d748a47227f3009473bee53829 Author: Frederik Heber 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 159102d9122f6d8a97f56ca41a68f71d8013ffcc Author: Frederik Heber Date: Tue Jul 7 03:08:58 2015 +0200 Fixing QtElementList::updateElement(). commit d786c35f4fdca6c5ed833969f1e384d06686d419 Author: Frederik Heber 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 955cea679b31b7874c93cb8d997b11bcaf2a16b6 Author: Frederik Heber Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit f8fbf47e3e35404ef8d057676712bf7e08878c3a Author: Frederik Heber 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 f508ef44a036e3bcaf921765c047e775c9607fb7 Author: Frederik Heber Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit 3d0f78ac353fd92f60f96ac7578dcfaf534df5c9 Author: Frederik Heber 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 7638f112755fa8ccbf1ec03cd2b7a4bd692e664b Author: Frederik Heber Date: Sun Jul 5 09:55:15 2015 +0200 Requiring now CodePatterns 1.3.0 due to ObservedValue. - also we purge the GlobalObservablesInfo in cleanUp(). commit 54ea665580c5d60071c56c7c23e6f0ba2aaa04bc Author: Frederik Heber Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit 721399df02f3fed601e321bd2f8318a06f620f48 Author: Frederik Heber 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 7ea2f4fd918e40dcc85187f510ea4fa8968cd7f8 Author: Frederik Heber Date: Sun Jul 19 18:13:44 2015 +0200 TESTFIX: selection molecule by name had escaped ticks. - also changed GuiCheck tests. commit 3a149d887a554e55eaf654a7381718ebde6729af Author: Frederik Heber 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 41b0262cf4600210ddb43b6155cb578146dcfcf5 Author: Frederik Heber Date: Wed Jul 8 12:33:49 2015 +0200 TESTFIX: regression test DepthFirstSearch had extra linebreak. commit 7eec7973958e249602381c3036847dda9f095ce9 Author: Frederik Heber Date: Wed Jul 8 08:47:52 2015 +0200 TESTFIX: atom selection regression tests with shapes were very noisy and hence very slow. commit 86064e74a1b91d855053d83bf0c6178dff98fb8a Author: Frederik Heber Date: Mon Jul 6 15:07:00 2015 +0200 TESTFIX: regression test SubgraphDissection Redo was broken. - also changed derived GuiChecks test. commit b79ab13124da2d9cf5984a6ab31dc3689637c2e2 Author: Frederik Heber 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 a9fdf2516f1720a0d0b4d1fdb0836cd5ceb08a68 Author: Frederik Heber 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 b81367a6d2a56f9b7ccdb045b35a230cc654abe7 Author: Frederik Heber 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 9a5bd55b56896a362384426f746349832c66b136 Author: Frederik Heber 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 0b2949c267c5c8e02d6281cdbf765ccc75b91191 Author: Frederik Heber 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 4a3a56a5c3d9a17d6ecdf86a6853016dd465c493 Author: Frederik Heber 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 0eef0fbe990c828bd747722af4e13e6dd33050ed Author: Frederik Heber 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 2176d048bdd2b382f48d92914755ef7a0fa9e272 Author: Frederik Heber Date: Sun Jul 19 12:03:05 2015 +0200 executePythonScriptFile() calls executePythonScript() now. commit f395492cef123ff81f9b1d2024fe29c9fe3a7e0e Author: Frederik Heber Date: Mon Jul 20 00:21:57 2015 +0200 FIX: QTUIFactory's test-single was not working right. commit 72cf5c1f2647d866aa467638eb837671d9f5942c Author: Frederik Heber Date: Fri Jun 19 19:35:50 2015 +0200 FIX: tests/regression FragmentationAutomation had a white space after line break. commit 2e516e1b584df3ca516bf7971bf24152c5cd6cab Author: Frederik Heber Date: Fri Jun 19 13:51:08 2015 +0200 FIX: Added molecuilderguitest to testsuite dependencies. commit 8491f32f212ad839f57f2ea401ab4d8d1a1264d9 Author: Frederik Heber 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. - added trianglematcher to testsuite dependencies. commit d4c8694f2cbd423faa6c19ddec88eeb7e5f118a3 Author: Frederik Heber Date: Thu Jun 18 03:53:26 2015 +0200 FIX: MakroAction's outputAsPython() uses outputAsPython() not outputAsCLI(). commit 9a48804bc9927b9c662e2653a5f08e7a1b65538b Author: Frederik Heber Date: Thu Jun 18 03:32:03 2015 +0200 FIX: QtMoleculeListView caused Command to be executed when selection changed internally. - we check via selecting but change is propagated via emit. Now we use DirectConnection. commit a87d1e2e1fdd4b7739a97a917c411937f941852d Author: Frederik Heber Date: Thu Jun 18 02:56:26 2015 +0200 FIX: ActionQueue::isIdle() states whether actions are executed or not. - QtUIFactory uses this to wait till test running next action. commit 9ec4b8fd1c0781bcd20ad52c2755ad52ae89d518 Author: Frederik Heber Date: Thu Jun 18 02:42:44 2015 +0200 FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account. commit bcf0561c44a090831a61ab4b4118c79b38750317 Author: Frederik Heber Date: Thu Jun 18 01:42:13 2015 +0200 FIX: QtTimeLine would cause another WorldSetTime action. - we did not catch where setValue() was called from, from an obtained Observable update() or from changing the slider. - QtTimeLine needs DirectConnection for valueChanged. commit 9fb2137ff4183dfa58b9083f255c8037873fb5ba Author: Frederik Heber Date: Thu Jun 18 01:41:07 2015 +0200 FIX: QtElementList now uses new updateElement(). - old refill() polls complete list of atoms of specific type in the moment an atom is destroyed ... now we only get informed about newly created atoms (safe) and changing elements (also safe). commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39 Author: Frederik Heber Date: Thu Jun 18 01:39:28 2015 +0200 TEMP: Removed QtLogBox for the moment. - ever and again causes SEGFAULT at QDebugStream::61 (QTextEdit::append()). commit ea73ce1f1f7bfca1ca449bed235f03c42b10b58b Author: Frederik Heber Date: Thu Jun 18 00:09:10 2015 +0200 Added QMutex to QtElementList for refill(). commit 7d0ddb4a2c0b433b55ce0a432f64c21bde6c9535 Author: Frederik Heber Date: Thu Jun 18 00:06:29 2015 +0200 FIX: QtMoleculeItem would not correctly signOff prior to molecule being destroyed. - all QtMoleculeItems signOn to molecule::AboutToBeRemoved. - getMolecule() may return NULL, is caught at two places. - getMoleculeId() for allowing QtMoleculeList to acess molid. commit 9d4f964574dae09a31c613751f654551f61f308a Author: Frederik Heber Date: Fri Jun 19 10:50:48 2015 +0200 FIX: QtHomologyList::refill() is now called via signal/slot. commit 7d0a4e076689218b5c7275f30d0ca5ee9341af8b Author: Frederik Heber Date: Wed Jun 17 19:15:04 2015 +0200 Storing the id of the main thread in static global variable. - this is preparatory for thread guard to be used in the context of Qt. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Tue Jul 28 16:04:27 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Tue, 28 Jul 2015 16:04:27 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch SeparatingOutQtThreads created. v1.4.11-58-g561b945 Message-ID: <20150728140427.25F3C5FD6E@saturn.ins.uni-bonn.de> 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, SeparatingOutQtThreads has been created at 561b94558bc3dbfbf79f15bb042f3376517efa4c (commit) - Log ----------------------------------------------------------------- commit 561b94558bc3dbfbf79f15bb042f3376517efa4c Author: Frederik Heber Date: Fri Jun 19 19:35:50 2015 +0200 FIX: tests/regression FragmentationAutomation had a white space after line break. commit f27c2c5f268ff6d130b9e9d54bc176a6377242d0 Author: Frederik Heber Date: Fri Jun 19 13:51:08 2015 +0200 FIX: Added molecuilderguitest to testsuite dependencies. commit 7d146a387231de6a2198a250dbdbab1f1e9076bd Author: Frederik Heber 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. - added trianglematcher to testsuite dependencies. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Tue Jul 28 16:04:34 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Tue, 28 Jul 2015 16:04:34 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue deleted. v1.4.11-107-gb47abff Message-ID: <20150728140434.40BEC5FD6E@saturn.ins.uni-bonn.de> 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 deleted was b47abff064ca6c1c30e67de797d8e0caeba61813 - Log ----------------------------------------------------------------- b47abff064ca6c1c30e67de797d8e0caeba61813 Revert "TEMP: Removed QtLogBox for the moment." ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Tue Jul 28 16:04:38 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Tue, 28 Jul 2015 16:04:38 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue created. v1.4.11-107-g3966610 Message-ID: <20150728140438.CE9185FD6E@saturn.ins.uni-bonn.de> 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 39666104810fa0b81def8a126ea8445b8f2d6d4c (commit) - Log ----------------------------------------------------------------- commit 39666104810fa0b81def8a126ea8445b8f2d6d4c Author: Frederik Heber Date: Sat Jul 25 15:06:15 2015 +0200 Revert "TEMP: Removed QtLogBox for the moment." This reverts commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39. commit 8c561c55ba862e01bdef54dafd4cf83c47235b55 Author: Frederik Heber 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 12dbabd298fcd1338f7e1891a77b04bba9cd14a1 Author: Frederik Heber 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 38ee22783079a415fc731fb17fdee33cbb575084 Author: Frederik Heber Date: Sun Jul 19 22:22:53 2015 +0200 FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more. commit 2c8c779e85fe26c183ee9f87b0f539a561bef1c5 Author: Frederik Heber 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 ec4c8a37c36a7bdea2a8f892683cb7fc55f0a3da Author: Frederik Heber Date: Sun Jul 19 15:47:57 2015 +0200 GLWorldScene lacked assert of Walker in atomClicked(). commit 4c71933b8751e3355f0767fe1db4b5cb3518d4e1 Author: Frederik Heber Date: Sun Jul 19 15:47:19 2015 +0200 Asserted that GLMoleculeObject_molecule::update() is never called. commit 3bb1aa6e77c7b976d33c3b65bd16e8ff2b52af09 Author: Frederik Heber Date: Sun Jul 19 15:46:41 2015 +0200 AddAtomBonds() now uses just id not ptr as param. commit 9f49a62ba351fb91b5a72a49774468eb58f66255 Author: Frederik Heber 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 71f131e47f77bae8ce1504c6acc83988d9dd7432 Author: Frederik Heber 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 d72ad91b6763f006918053bc544fd3bbea3e2eb4 Author: Frederik Heber 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 449a75cd1ecee1ed5d470b813ff060e35901bb1d Author: Frederik Heber 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 926d009fde2bddd25abd80ac9d8c836ce89229be Author: Frederik Heber 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 42fa5848022065adc2d06cb88259ce9748bfe172 Author: Frederik Heber 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 a6b1ff153a59d5396e615441f550b981712805c6 Author: Frederik Heber 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 00ed60391ed81d42344d494241a3d714ba0a19dd Author: Frederik Heber 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 9c55f8c068989047ca8e219489e7749f37e5541b Author: Frederik Heber 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 d151d9f4db336233533f226f2ce8e33a305f6db5 Author: Frederik Heber 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 1f87cf2f825c279756c9529dd6d3ec464ec4b374 Author: Frederik Heber Date: Thu Jul 16 01:25:22 2015 +0200 Qt4 instance use new lastChanged..Id() in place of lastChanged(). commit aae4965e5b1ea1ca3c0393f7222712ea13503328 Author: Frederik Heber Date: Thu Jul 16 01:23:30 2015 +0200 Added lastChanged..Id() to both World and molecule. commit f3b10dbe5c43e14ebe224a79fa9d9773a3c610e2 Author: Frederik Heber 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 eae257505aca7293f14e3ce7fa082bc103f3a5d8 Author: Frederik Heber Date: Wed Jul 15 16:01:41 2015 +0200 GLWorldView does not emit changed() on each general update() from the World and others. commit d57818b17812190b2314bce6248c969cf31287ec Author: Frederik Heber Date: Wed Jul 15 15:56:58 2015 +0200 DOCU: Updated documentation on Qt Gui construct. commit cc970e835c844b58febe62c0f93e724c18630531 Author: Frederik Heber 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 209ad6b35174e0f5a9e1b1c830879c805c525fe9 Author: Frederik Heber Date: Fri Jul 10 12:54:51 2015 +0200 Using static Observable::..NotificationsChannel() functions. commit 30842d3369ac305ebdfd515dd9d27ebfd62eac6d Author: Frederik Heber 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 1743af8f64dfbe667b6e6d9a91801bbaee471b16 Author: Frederik Heber Date: Tue Jul 7 03:08:58 2015 +0200 Fixing QtElementList::updateElement(). commit c5c7c71c37cd761f197da27c0aaa1fdea2a36a14 Author: Frederik Heber 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 ba4c71caed50d2eecd35c99adc47613ac0534f59 Author: Frederik Heber Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit 5930513559ef8e3ff884ab4fc9eb20b16ea64776 Author: Frederik Heber 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 ec008cfa3ecb1ca565339d0334ac9f7b14efa729 Author: Frederik Heber Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit 7df9125edabcd62fc91a5c0274168f49cc1eaab4 Author: Frederik Heber 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 27a26ff8bc8cd9796e1d2b737696a839a8c6a723 Author: Frederik Heber Date: Sun Jul 5 09:55:15 2015 +0200 Requiring now CodePatterns 1.3.0 due to ObservedValue. - also we purge the GlobalObservablesInfo in cleanUp(). commit efc3553d8a6c21749d2a3cf049d7e228874464ef Author: Frederik Heber Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit db3075da45a02e6e71335b33e873d2de5b6371cb Author: Frederik Heber 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 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 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 Date: Wed Jul 8 12:33:49 2015 +0200 TESTFIX: regression test DepthFirstSearch had extra linebreak. commit 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764 Author: Frederik Heber 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 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 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 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 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 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 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 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 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 Date: Sun Jul 19 12:03:05 2015 +0200 executePythonScriptFile() calls executePythonScript() now. commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781 Author: Frederik Heber Date: Mon Jul 20 00:21:57 2015 +0200 FIX: QTUIFactory's test-single was not working right. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 29 20:15:40 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 29 Jul 2015 20:15:40 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue deleted. v1.4.11-107-g3966610 Message-ID: <20150729181540.CB0E25FD6E@saturn.ins.uni-bonn.de> 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 deleted was 39666104810fa0b81def8a126ea8445b8f2d6d4c - Log ----------------------------------------------------------------- 39666104810fa0b81def8a126ea8445b8f2d6d4c Revert "TEMP: Removed QtLogBox for the moment." ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Wed Jul 29 20:15:45 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Wed, 29 Jul 2015 20:15:45 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue created. v1.4.11-107-ga4c720b Message-ID: <20150729181545.509115FD6E@saturn.ins.uni-bonn.de> 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 a4c720ba326e1744e9886eb2f7e204c57a33fac6 (commit) - Log ----------------------------------------------------------------- commit a4c720ba326e1744e9886eb2f7e204c57a33fac6 Author: Frederik Heber Date: Sat Jul 25 15:06:15 2015 +0200 Revert "TEMP: Removed QtLogBox for the moment." This reverts commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39. commit cd076e0a256acaa8c530169b28273b28fdcca238 Author: Frederik Heber 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 0d1b86b36be06e0501667a804af0fad448000cb8 Author: Frederik Heber 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 5e37c55ee570e3454d8e68fe7f7794d35f7b932c Author: Frederik Heber Date: Sun Jul 19 22:22:53 2015 +0200 FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more. commit bf038d558b05deeccd28f5ddd2eb3628e003d428 Author: Frederik Heber 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 dc73e4ac38cf4a7fa9b47edfb6151ca317ead3d8 Author: Frederik Heber Date: Sun Jul 19 15:47:57 2015 +0200 GLWorldScene lacked assert of Walker in atomClicked(). commit e9d386944fe04b9f8f669996280294efa5656074 Author: Frederik Heber Date: Sun Jul 19 15:47:19 2015 +0200 Asserted that GLMoleculeObject_molecule::update() is never called. commit 66232fa95e5e4e7f505d102fd4bf8d7a39ba61f2 Author: Frederik Heber Date: Sun Jul 19 15:46:41 2015 +0200 AddAtomBonds() now uses just id not ptr as param. commit b6818c443541ae848b25c56aa5dcfaf06453f594 Author: Frederik Heber 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 a918f46972de0a708fe558f3f2bbc1f097fd4400 Author: Frederik Heber 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 d3f7a102f4c793fc2c676581d5b2a2fe39895aed Author: Frederik Heber 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 79058b20454891ac2b22bb9015d758d9bc2d0a41 Author: Frederik Heber 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 325910f5d914384f151277c5e7b78c9a545ad873 Author: Frederik Heber 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 d01666d999133f2bb654f9c30f6ce3ed0792cf2b Author: Frederik Heber 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 886e371a581205b08c48ca46c4468861bc39957d Author: Frederik Heber 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 ac18e61ba9cd79ea7ac90d384762922befbce361 Author: Frederik Heber 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 f90076b4aa1ad9f3db430bb6bf119e4860edf7a4 Author: Frederik Heber 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 9960c72b1c234242b1f9866c3075eae2aae6ce24 Author: Frederik Heber 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 bb0f155cfa056ce9298ef704ed931b8ca277d754 Author: Frederik Heber Date: Thu Jul 16 01:25:22 2015 +0200 Qt4 instance use new lastChanged..Id() in place of lastChanged(). commit f88eaa9133359a3fc276bd9ba74b8c0125b6339e Author: Frederik Heber Date: Thu Jul 16 01:23:30 2015 +0200 Added lastChanged..Id() to both World and molecule. commit 17f7a5cb8ef33e8cc75c298b448eba9cc9e9e9fa Author: Frederik Heber 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 d75db8ffdd7d9c9c14f9088c44e8c9d0e0b1c11e Author: Frederik Heber Date: Wed Jul 15 16:01:41 2015 +0200 GLWorldView does not emit changed() on each general update() from the World and others. commit ef3c77f9fe7d6048aa18d0277661991a6ba7d5d3 Author: Frederik Heber Date: Wed Jul 15 15:56:58 2015 +0200 DOCU: Updated documentation on Qt Gui construct. commit 4ce565d73cabe94ffae052b21d3e1ef951bf3aca Author: Frederik Heber 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 9cb0e8db2e8302aadbc74e4a5dad80811b458c34 Author: Frederik Heber Date: Fri Jul 10 12:54:51 2015 +0200 Using static Observable::..NotificationsChannel() functions. commit 9217e32ffce1a96b48f2e76dd9c24de9b61592c0 Author: Frederik Heber 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 f18b3abe192a40966c059b3b0fe8cd29aca68be2 Author: Frederik Heber Date: Tue Jul 7 03:08:58 2015 +0200 Fixing QtElementList::updateElement(). commit f57f269fde580fed4bbcd7fc303cc6a6848b3c86 Author: Frederik Heber 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 6628bf4c396a379c0321b48624e318cb30e3bf85 Author: Frederik Heber Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit 937cc07ec420842ead17e82ebab78835c299c887 Author: Frederik Heber 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 8a3a0ecc89672e9c80b1c6f0571706960be90e06 Author: Frederik Heber Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit ccfbd448498958622c63355c8b71b5ac73da5392 Author: Frederik Heber 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 213bcd25f3b16f369e288012a97813f8fb499515 Author: Frederik Heber Date: Sun Jul 5 09:55:15 2015 +0200 Requiring now CodePatterns 1.3.0 due to ObservedValue. - also we purge the GlobalObservablesInfo in cleanUp(). commit 088e90f1f9f7d019dd765bbc5c66070a57fffd37 Author: Frederik Heber Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit c66ae6684084ff864820af9b907d9f3b9725530d Author: Frederik Heber 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 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 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 Date: Wed Jul 8 12:33:49 2015 +0200 TESTFIX: regression test DepthFirstSearch had extra linebreak. commit 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764 Author: Frederik Heber 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 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 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 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 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 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 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 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 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 Date: Sun Jul 19 12:03:05 2015 +0200 executePythonScriptFile() calls executePythonScript() now. commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781 Author: Frederik Heber Date: Mon Jul 20 00:21:57 2015 +0200 FIX: QTUIFactory's test-single was not working right. ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Thu Jul 30 22:43:25 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Thu, 30 Jul 2015 22:43:25 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue deleted. v1.4.11-107-ga4c720b Message-ID: <20150730204325.AB6255FD6E@saturn.ins.uni-bonn.de> 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 deleted was a4c720ba326e1744e9886eb2f7e204c57a33fac6 - Log ----------------------------------------------------------------- a4c720ba326e1744e9886eb2f7e204c57a33fac6 Revert "TEMP: Removed QtLogBox for the moment." ----------------------------------------------------------------------- hooks/post-receive -- From git at ins.uni-bonn.de Thu Jul 30 22:43:33 2015 From: git at ins.uni-bonn.de (git at ins.uni-bonn.de) Date: Thu, 30 Jul 2015 22:43:33 +0200 (CEST) Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue created. v1.4.11-106-gf4dee7e Message-ID: <20150730204333.B16425FD6E@saturn.ins.uni-bonn.de> 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 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 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 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 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 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 Date: Sun Jul 19 15:47:57 2015 +0200 GLWorldScene lacked assert of Walker in atomClicked(). commit 9689958e7cf83fc56bd3ce101b4e2377812bbdcc Author: Frederik Heber Date: Sun Jul 19 15:47:19 2015 +0200 Asserted that GLMoleculeObject_molecule::update() is never called. commit 4999cc1bdc8e0dc998b84667d9ac76e074740559 Author: Frederik Heber Date: Sun Jul 19 15:46:41 2015 +0200 AddAtomBonds() now uses just id not ptr as param. commit bb3c6395fc5644893150017d8d77267f10f341ce Author: Frederik Heber 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 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 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 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 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 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 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 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 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 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 Date: Thu Jul 16 01:25:22 2015 +0200 Qt4 instance use new lastChanged..Id() in place of lastChanged(). commit 560fde03092bed821426b2947d5ed75433a9f5ce Author: Frederik Heber Date: Thu Jul 16 01:23:30 2015 +0200 Added lastChanged..Id() to both World and molecule. commit 74eca4ad3c549f66044ae4c6e9f516b06b657004 Author: Frederik Heber 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 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 Date: Wed Jul 15 15:56:58 2015 +0200 DOCU: Updated documentation on Qt Gui construct. commit 7ec5b58a4b1f90c652d45fd9a7e5b880d0128d69 Author: Frederik Heber 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 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 Date: Tue Jul 7 03:08:58 2015 +0200 Fixing QtElementList::updateElement(). commit b1edc5e445b076a4f6a98cc2ad6351fae695782e Author: Frederik Heber 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 Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit 7a7d0aed5391ad7c8f1eda65f06dfd6e8355609c Author: Frederik Heber 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 Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit cc2dc6d9e9e20e77513818ccde1e884d51353f1b Author: Frederik Heber 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 Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit 92be0d3e0a4164d2d47d5f705fc955cf12f899b9 Author: Frederik Heber 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 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 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 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 Date: Wed Jul 8 12:33:49 2015 +0200 TESTFIX: regression test DepthFirstSearch had extra linebreak. commit 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764 Author: Frederik Heber 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 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 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 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 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 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 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 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 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 Date: Sun Jul 19 12:03:05 2015 +0200 executePythonScriptFile() calls executePythonScript() now. commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781 Author: Frederik Heber Date: Mon Jul 20 00:21:57 2015 +0200 FIX: QTUIFactory's test-single was not working right. ----------------------------------------------------------------------- hooks/post-receive --