- Molecuilder-devel

[SCM] annotated tag v1.5.0 created. v1.5.0
by git＠ins.uni-bonn.de 15 Aug '15

15 Aug '15

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, v1.5.0 has been created at 86a5ee025241f95111ddb323821c85944821f2c2 (tag) tagging bff5e273091c20e062b35677796d4f022e572385 (commit) replaces v1.4.12 tagged by Frederik Heber on Thu Aug 13 23:53:45 2015 +0200 - Log ----------------------------------------------------------------- GuiChecks regression tests are all fully working (1% crashes tolerated for the moment). This version contains the following branches: bff5e27 Candidate_v1.5.0 (Setting version) 66b092e DebianPackaging (adding debian files for creating a .deb package file) 6fe4f76 GUIStates_using_ObservedValue (ObservedValue cashes a state in the World even beyond the instance's destruction, e.g. the position of an atom, which allows to have Qt and World run in separate threads) Frederik Heber (47): Using static Observable::..NotificationsChannel() functions. Removed init() and signal WorldSelectionChanged() from GLWorldScene. GLMoleculeObject_atom uses ObservedValue for internally representing atom's state. GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. QtMoleculeItem_... use ObservedValue for internally representing atom's state. GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. GLWorldScene propagates changed mol id to GLMoleculeObject_molecule. Fixing QtElementList::updateElement(). QtMoleculeList::informDirtyState() does not need to lock refill_mutex anymore. Fixing QtMoleculeList with list containing only formulas and ids. DOCU: Updated documentation on Qt Gui construct. GLWorldView does not emit changed() on each general update() from the World and others. GLWorldView no longer listens to WorldTime::TimeChanged. Added lastChanged..Id() to both World and molecule. Qt4 instance use new lastChanged..Id() in place of lastChanged(). Removed molecule::lastChanged(). World now first releases id and then destroys the atom/molecule. FIX: Fixing "pure virtual function called" in QtMoleculeItem. QtMoleculeItem_.. now shout when they receive subjectKilled(). Added QtSelectionChangedAgent to transform O/O to S/S system. QtMainWindow uses QtSelectionChangedAgent. Fixed formula usage in Qt part of code. FIX: Setting molecule's name via QtMoleculeList item is again possible. GLMoleculeObject_molecule also has ObservedValue for name. GLMoleculeObject_molecule does not use getAtomCount() anymore. Avoided use of getId() on molecules and atoms in Qt code where possible. AddAtomBonds() now uses just id not ptr as param. Asserted that GLMoleculeObject_molecule::update() is never called. GLWorldScene lacked assert of Walker in atomClicked(). FIX: Fixing display of shapes in GLWorldView. FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more. FIX: GLMoleculeObject_bond had both flipped ids and the side. TESTFIX: Marked molecule translation guicheck tests as XFAIL. FIX: QtLogBox is again included and working thread-safe. FIX: updateBoundingBox() must not call molecule::getBoundingBox() on every update. FIX: AllPotentialHealder.hpp not excluded from CodeCheck config_h. DOCU: Described workaround for missing pyconfig.h. FIX: bash_completion was accidentally removed by clean target. Added debian/.. files for debian packaging. Added script for creating debian package. Enabled GUI compilation for debian package. Added debugging package molecuilder-dbg and source package molecuilder-dev DISTFIX: EXTRA_DIST in tests/../Makefile.ams depended on not yet set variables. FIX: Qt can now be found even without --with-Qtbin... TESTFIX: for source builds we need to exclude all moc'ed files from codechecks. FIX: This prevent crash of molecuildergui in debian package. Set version to 1.5.0. ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] annotated tag v1.4.12 created. v1.4.12
by git＠ins.uni-bonn.de 05 Aug '15

05 Aug '15

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, v1.4.12 has been created at 8040ff39e1fe7f4360fc961e0654a1734273e821 (tag) tagging 0ea4ddbf6833adf1a4a2ada1981935715775879f (commit) replaces v1.4.11 tagged by Frederik Heber on Wed Aug 5 09:12:47 2015 +0200 - Log ----------------------------------------------------------------- Preliminary version for working guicheck tests. This version contains the following branches: 0ea4ddb Candidate_v1.4.12 (dist fixes, mem fixes and cleaning of Action and related interfaces) c66ae66 GuiCheck_TestFixes (several test fixes such that guicheck regression tests are properly constructed via the create script) 561b945 SeparatingOutQtThreads (Adding mutexes in Qt code parts for a start) 9ad4d61 AddingConstDescriptors (descriptors now allow const access, hence they don't cause updates via ObservedIterators, many World getters to atoms and molecules now have explicit const versions) a4dee7c Fixing_MolecuilderGui (Initial GUI fixes) Frederik Heber (80): FIX: Regression test set-parameters-mpqc undo compared against wrong file. FIX: parser-parameters in regression tests basis and maxiter contained white spaces. FIX: print on CommandHelp("help") not required in python regression test. Gui is returning error code of 5 (in test mode) if (last) action failed. GLWorldScene::moleculeInserted() gets moleculeId_t as param. GLWorldScene::atomInserted() also adds NULL object to ..inSceneMap. FIX: QtMoleculeListView::moleculeSelected() did not check for presence of molitem. FIX: GLWorldScene::changeAtomId() reinserted with oldid instead of newid. Fixed ObserverLog message in GLWorldView. FIX: World does not to heed updates from internal MoleculeListClass. Changed hoverChanged() from mol* to moleculeId_t. QtMoleculeItem now uses moleculeId_t instead molecule*. QtElementList now listens to AtomObserver and not MoleculeListClass anymore. FIX: World does not sign on to molecule changes. Molecule has new channel FormulaChanged used by specific QtMoleculeItem. tempcommit: Attempt to replace QtElementList::refill() by faster system. FIX: createGuiChecks can handle multi-lines. DOCU: Corrected userguide. FIX: molecule's Formula is not changed when atom changes element. atom::getMolecule() now returns ptr to const molecule. World::getMolecules..() now has const versions as well. World::getAtoms() now has const versions as well. Replaced getMolecule() by const access version where possible. Replaced World::getAllMolecules() wherever possible by const version. Replaced World::getAtom() wherever possible by const version. Replaced World::getAllAtoms() by const version where possible. Replaced all World::getSelected...() to const version where possible. Converted FormatParser::save() to using vector of const atom ptrs. FIX: GLMoleculeObject_molecule() may overlap with atomInserted() signal. FIX: QtInfoBox now works mostly on ids. FIX: QtElementList does not have a changed() signal. FIX: GLMoleculeObject_molecule was not informed of atom index change. Removed lots of code in GLWorldScene that now resides in GLMoleculeObject_molecule. UIs are now initialized before any action takes place. Removed GLMoleculeObject_molecule's init() and reinit(). FIX: GLWorldScene/View capture all missed signals for each GLMoleculeObject_molecule. FIX: GLWorldView must not listen to moleculeRemoved but to its subjectKilled. FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted. QtInfoBox updates information on update signal. FIX: QDebugStream is now thread-safe. Extracted signing on to molecule into activateObserver. FIX: GLWorldScene did not initialize SelectionMode properly. FIX: GLWorldView was signed in to atomInserted and atomRemoved without any need. FIX: QtUIFactory copied to wrong argv. Storing the id of the main thread in static global variable. FIX: QtHomologyList::refill() is now called via signal/slot. FIX: QtMoleculeItem would not correctly signOff prior to molecule being destroyed. Added QMutex to QtElementList for refill(). TEMP: Removed QtLogBox for the moment. FIX: QtElementList now uses new updateElement(). FIX: QtTimeLine would cause another WorldSetTime action. FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account. FIX: ActionQueue::isIdle() states whether actions are executed or not. FIX: QtMoleculeListView caused Command to be executed when selection changed internally. FIX: MakroAction's outputAsPython() uses outputAsPython() not outputAsCLI(). Added TriangleMatcher to safely compare tesselation .dat files. FIX: Added molecuilderguitest to testsuite dependencies. FIX: tests/regression FragmentationAutomation had a white space after line break. FIX: QTUIFactory's test-single was not working right. executePythonScriptFile() calls executePythonScript() now. Group item with atom count of 0 is confusing in QtMoleculeList, creating with empty string. FIX: atom_bondedparticle signatures changed to more const versions. FIX: Molecule has new signal IndexChanged. FIX: atom_atominfo lacked some notifies or had them wrong. Added getSelected..Ids() for both atoms and molecules. Added Action::setOptionValue() which allows setting the option via a string. Added TriangleMatcher to safely compare tesselation .dat files. TESTFIX: regression test SubgraphDissection Redo was broken. TESTFIX: atom selection regression tests with shapes were very noisy and hence very slow. TESTFIX: regression test DepthFirstSearch had extra linebreak. FIX: Added Parameters Value_Elements to correctly set vector of elements from string. TESTFIX: selection molecule by name had escaped ticks. TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in save-adjacency regression test. DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am. DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not bin_... FIX: Adjacency's operator<<() printed fixed number (3) of entries. Action::isActive() is now const member function. Cleaned up ActionQueue's interface: Actions are always cloned. DOCU: Enhanced description of test policy on version update. Set version to v1.4.12. ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] branch Candidate_v1.4.12 created. v1.4.11-80-g0ea4ddb
by git＠ins.uni-bonn.de 05 Aug '15

05 Aug '15

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_v1.4.12 has been created at 0ea4ddbf6833adf1a4a2ada1981935715775879f (commit) - Log ----------------------------------------------------------------- commit 0ea4ddbf6833adf1a4a2ada1981935715775879f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 2 14:05:47 2015 +0200 Set version to v1.4.12. commit c307ba4e4b46954d39964089972d5cb1f29a6f40 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 2 14:01:05 2015 +0200 DOCU: Enhanced description of test policy on version update. commit 10aee4386f0c1b8e07b3a74e7d97d99ef2622bc8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 3 11:25:02 2015 +0200 Cleaned up ActionQueue's interface: Actions are always cloned. - Action's dstor needs to be public as we have a clone() function. - ActionRegistrys' (and AQ's) getActionByName now returns const ref. We must not return a ptr as it may not get deleted elsewhere. We are handing out prototypes. - queueAction(action*,...) is private to prevent leakage, queueAction(string, ...) is the public interface. - some other small functions are now private, too. - MakroActions now need to clone() the prototype on prepare() and delete them on unprepare(). - ActionSequence deletes contained actions. - FIX: ActionSequenceUnitTest cannot check on not-called property of removed actions anymore as these are gone now (they are deleted on removal and they are cloned on insertion). - DOCU: Updated documentation on Actions. commit 94232b82bf9b20300fb870881f38c94ce0857bdd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 3 11:20:16 2015 +0200 Action::isActive() is now const member function. - also changed TextMenu's items. - mutexes in ActionQueue are now mutable. commit 725a1da23441218ebfe802d5508feedc1a4a8b46 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 19:09:47 2015 +0200 FIX: Adjacency's operator<<() printed fixed number (3) of entries. - this caused seg violations and occurred through memcheck run. - it was a copy&paste error from trianglematcher's. commit 3532b77102b83baecdd39fade5a59f5aaf230ed0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 12:21:56 2015 +0200 DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not bin_... - as such they are not installed and hence .in files must not use AUTOTEST_PATH but topdir (top build directory). - also in GuiChecks, regresssion, and Tesselations tests TESTSUITE was made dependent on them but target check and installcheck only actually depend on the wrapper scripts (molecuilder, ...). commit 8e790ebd981dac78daa03f5e06560ba8ea84a21a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 11:27:06 2015 +0200 DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am. commit c66ae6684084ff864820af9b907d9f3b9725530d Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Sun Jul 19 12:03:05 2015 +0200 executePythonScriptFile() calls executePythonScript() now. commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 20 00:21:57 2015 +0200 FIX: QTUIFactory's test-single was not working right. commit 561b94558bc3dbfbf79f15bb042f3376517efa4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 13:51:08 2015 +0200 FIX: Added molecuilderguitest to testsuite dependencies. commit 7d146a387231de6a2198a250dbdbab1f1e9076bd Author: Frederik Heber <heber(a)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. - added trianglematcher to testsuite dependencies. commit d4c8694f2cbd423faa6c19ddec88eeb7e5f118a3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:53:26 2015 +0200 FIX: MakroAction's outputAsPython() uses outputAsPython() not outputAsCLI(). commit 9a48804bc9927b9c662e2653a5f08e7a1b65538b Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:09:10 2015 +0200 Added QMutex to QtElementList for refill(). commit 7d0ddb4a2c0b433b55ce0a432f64c21bde6c9535 Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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 <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 10:50:48 2015 +0200 FIX: QtHomologyList::refill() is now called via signal/slot. commit 7d0a4e076689218b5c7275f30d0ca5ee9341af8b Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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. commit 9ad4d612899bb1547d6400f43c8330480c78d103 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 20 00:05:41 2015 +0200 FIX: QtUIFactory copied to wrong argv. commit 2a4b054470c32d7dfd7235c070c54dcdde1a99a0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 19:01:13 2015 +0200 FIX: GLWorldView was signed in to atomInserted and atomRemoved without any need. commit 9b56f0a18eb8b397e931302e9b49b96672885279 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 19:00:55 2015 +0200 FIX: GLWorldScene did not initialize SelectionMode properly. commit 73b13cdd45329e4acbf0a0ca9dd9b780dac892d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 18:59:19 2015 +0200 Extracted signing on to molecule into activateObserver. - is called by GLWorldScene after all "missed" signals have been emitted. commit 9737db9c0d2798f3bb61807cda1a59701dc33939 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 18:58:32 2015 +0200 FIX: QDebugStream is now thread-safe. - also Fix to QTextCursor not registered. commit 4965922285cce1bd99002053cab2e8913e7fd819 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 16 20:37:07 2015 +0200 QtInfoBox updates information on update signal. commit 2f76d207662ae0c1e550c622a0d53f769646a691 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 15 23:01:19 2015 +0200 FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted. commit f759e5f2aa47178e7225d67a127028ed62570fdc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:24:00 2015 +0200 FIX: GLWorldView must not listen to moleculeRemoved but to its subjectKilled. - atoms of a molecule a removed after moleculeRemoved which only gives a prior note about the removal. Then, we are flooded with atomRemoved for each of its atom which go into MoleculeMissedStateMap and pop up when a same-id molecule is instantiated, causing assert failures. commit 9c259e4ccaa1f9c8cabd00d1c1ca8e22e40a8199 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 11 09:33:58 2015 +0200 FIX: GLWorldScene/View capture all missed signals for each GLMoleculeObject_molecule. - Taking note of subscribed molecules to sign Off on GLWorldView's destruct. - GLWorldView::recieveNotification() is checking for whether molecule actually exists still. commit 8923ad833541d0d5da649e21cb7b6537558a282b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 8 19:05:01 2015 +0200 Removed GLMoleculeObject_molecule's init() and reinit(). - also removed InitAtomMap and associated code. - removed changeAtomId slot/signal in GLWorldScene. commit 28864c30d2f893d3d3b12899626e0d2defa2da74 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 8 18:26:34 2015 +0200 UIs are now initialized before any action takes place. - UIFactory::doneInitializing() is set after mainwindow is instantiated. - QTUIFactory::testrun() waits till UI is done initializing. commit d619338ee65ee4df303696fa8a82dbf27e594f44 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 19:11:15 2015 +0200 Removed lots of code in GLWorldScene that now resides in GLMoleculeObject_molecule. - atoms and their bonds are now controlled by the latter. commit 8d3ee64e6d4d84d033921af0895634eccaec7466 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 19:10:49 2015 +0200 FIX: GLMoleculeObject_molecule was not informed of atom index change. commit 084304e6dfbb4c6567df7dac36d3cb925b2a0b8e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 14:45:20 2015 +0200 FIX: QtElementList does not have a changed() signal. commit e7341ec2716284e96e58763befbd8fa9e68b27df Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 13:23:35 2015 +0200 FIX: QtInfoBox now works mostly on ids. - slots are requested as ..Id_t and not as ptrs anymore for some time. commit f3b5971ec8cc96538608d12dd2998861f1e187db Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 12:41:40 2015 +0200 FIX: GLMoleculeObject_molecule() may overlap with atomInserted() signal. - this is because GLMoleculeObject_molecule takes some time till init() is called and its runs in a separate thread (hence, further atoms may be loaded into the just created atoms). As we first signOn() and then call init(), we may end up initializing atoms whose atomInserted signal then also comes in but lateron. This causes the AtomsInSceneMap to have double entries and the assertion to fail. We now keep book of all atomic ids inserted during init() and these are ok to appear doubly and their signal is skipped. commit fac58f919238a82bc5d6cab2eb5c9621c85c941c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 10:52:11 2015 +0200 Converted FormatParser::save() to using vector of const atom ptrs. - required to change all save() functions in all parsers. commit 99db9baca1782e208fb17d2cc6ace3f4cadb568b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 10:32:10 2015 +0200 Replaced all World::getSelected...() to const version where possible. - also added const version of World::getSelectedAtoms(). commit a58c16f47065e9446b7916a407271c6544180022 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:16:02 2015 +0200 Replaced World::getAllAtoms() by const version where possible. commit f01769bf04baacedde88443ce16ab2f2dd809f30 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 18:57:36 2015 +0200 Replaced World::getAtom() wherever possible by const version. - some AtomSet member functions now have const atom ptr instead of atom ptr. - molecule can return const and non-const AtomSet. - added FromIdToConstAtom to allow iterate through atoms in molecule (which are stored by id, not by ptr) in const fashion. - in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const (because copying involves father atom who is stored non-const). commit 1259df9500410b59c3a56d9cf8d54624b53f97da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 10:56:36 2015 +0200 Replaced World::getAllMolecules() wherever possible by const version. commit 63fb7a963007e0f94b955d96ca949cd435eacb2a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 10:48:35 2015 +0200 Replaced getMolecule() by const access version where possible. - so far this is done done via const_casting the World. commit 795c0fbd35ce4d14a5986636e88a0fe5fcc53381 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 10:30:56 2015 +0200 World::getAtoms() now has const versions as well. - this in turn required to adapt all AtomDescriptors and some fixes, e.g. predicate is now const member and works on const atom ptr. commit 97445f1edda30c6d17472c562f9832a49df3e644 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 09:42:00 2015 +0200 World::getMolecules..() now has const versions as well. - this required to adapt all MoleculeDescriptors accordingly. commit 270bdface47b2d970089daba2ed78dc3f90395a7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 09:22:29 2015 +0200 atom::getMolecule() now returns ptr to const molecule. - changed some places where getMolecule() was used. Most of them required only const access anyway. World is allowed to const'cast the constness away as it commands over molecules anyway. commit 9b3262b2e3b9296a0c5ea340ffa6b8b38a694615 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 12:43:49 2015 +0200 FIX: molecule's Formula is not changed when atom changes element. commit d12d818e7c101fa705af778bca10771e52c18690 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 09:42:19 2015 +0200 DOCU: Corrected userguide. - this still needs some more work, e.g. w.r.t to code snippets indentation. commit 599b3232e65ac3b245869d9dd63c45d7e8f162f4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:53:44 2015 +0200 FIX: createGuiChecks can handle multi-lines. - also we reduce verbosity by default. - redid all GuiCheck test scripts. commit a4dee7ca90a18a6be133d405f7a0b0f5e8181d6d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 18:00:52 2015 +0200 tempcommit: Attempt to replace QtElementList::refill() by faster system. - this is not finished or tested as it is incompatible right now right refill(). commit 6b69594bcabc35afd7ab6ba170e610a1588c1df4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 18:01:34 2015 +0200 Molecule has new channel FormulaChanged used by specific QtMoleculeItem. commit 74831898be603d80e0fe28f09943254aee55e893 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 17:59:56 2015 +0200 FIX: World does not sign on to molecule changes. commit 6b474e1aa04d153d6d0b68b8cf8de9ed806ef258 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 17:09:31 2015 +0200 QtElementList now listens to AtomObserver and not MoleculeListClass anymore. commit 69b434b1d1a5180a87c3d669024542593104c8e0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 22 23:14:50 2015 +0200 QtMoleculeItem now uses moleculeId_t instead molecule*. commit 704d59ccf5f2559ab48b197552d1bea827b92ad2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 22 22:18:58 2015 +0200 Changed hoverChanged() from mol* to moleculeId_t. - also changed signatures for atom. commit 34641b910ee6b9ce05b01bd6c5aa2e558ef54466 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 22:56:56 2015 +0200 FIX: World does not to heed updates from internal MoleculeListClass. - there is not even an World::update() nor ::recieveNotifications(). commit eac542d5b19b04687918ad9252e1d9cb4adfc4cd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 22:56:40 2015 +0200 Fixed ObserverLog message in GLWorldView. commit 2520ccbe1eb2cf5456bd770eedc0656bcef7846f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:57:49 2015 +0200 FIX: GLWorldScene::changeAtomId() reinserted with oldid instead of newid. - also fixed assertion message in GLMoleculeObject_molecule::atomInserted(). commit ec6abc5fcbede9d754e9e8267ef3dc93f92ab49a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:05:31 2015 +0200 FIX: QtMoleculeListView::moleculeSelected() did not check for presence of molitem. commit 4669341c36fbec6d4f4114ed868a2c6ca3c34085 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:04:49 2015 +0200 GLWorldScene::atomInserted() also adds NULL object to ..inSceneMap. commit ef3013cd854f882cf600cfb78dc0c9cd4f78897b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 19:37:52 2015 +0200 GLWorldScene::moleculeInserted() gets moleculeId_t as param. - we must not use pointers to instances outside the Qt world as parameters. - we add NULL into MoleculesInSceneMap for moleculeRemoved to remove the entry. commit c13b913f78b416eebfc6ff8ac0031329a4944e78 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue May 19 07:28:36 2015 +0200 Gui is returning error code of 5 (in test mode) if (last) action failed. - this allows to take over return code checks in testsuite. commit 068a852341119fad16f4f312d9ab6289fe0edd65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 14:30:06 2015 +0200 FIX: print on CommandHelp("help") not required in python regression test. - also fixed double disclaimer. commit 7774f7e70f2ae517967d41e9125f5dba0adf1dbe Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:58:20 2015 +0200 FIX: parser-parameters in regression tests basis and maxiter contained white spaces. commit 23110a4092c457be30e89f88181ea2df46c504e5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 10:04:04 2015 +0200 FIX: Regression test set-parameters-mpqc undo compared against wrong file. - functionality is actually working and removed XFAIL_IF. - regression test set-parameters-mpqc had too many white spaces in parser-parameters. ----------------------------------------------------------------------- hooks/post-receive --

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[SCM] branch Candidate_v1.4.12 deleted. v1.4.11-81-g9247f61
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[SCM] branch Candidate_v1.4.12 updated. v1.4.11-81-g9247f61
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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_v1.4.12 has been updated via 9247f6140e2d96abe74afa09ec2b9ab4a9604c10 (commit) from 3107c8ac84207e4525807b9151d2d08674118a2c (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 9247f6140e2d96abe74afa09ec2b9ab4a9604c10 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 5 00:21:02 2015 +0200 FIX: ActionQueue::isIdle() const nees mutable mutex. ----------------------------------------------------------------------- Summary of changes: src/Actions/ActionQueue.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) hooks/post-receive --

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[SCM] branch SeparatingOutQtThreads deleted. v1.4.11-58-g561b945
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[SCM] branch GUIStates_using_ObservedValue deleted. v1.4.11-106-gf4dee7e
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[SCM] branch Candidate_v1.4.12 created. v1.4.11-80-g3107c8a
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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_v1.4.12 has been created at 3107c8ac84207e4525807b9151d2d08674118a2c (commit) - Log ----------------------------------------------------------------- commit 3107c8ac84207e4525807b9151d2d08674118a2c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 2 14:05:47 2015 +0200 Set version to v1.4.12. commit c0068c29883ab89f29f1ad36a44aa546d131cc6a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 2 14:01:05 2015 +0200 DOCU: Enhanced description of test policy on version update. commit 82d111988cb6e74d73ae5383787080b17bf2cce6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 3 11:25:02 2015 +0200 Cleaned up ActionQueue's interface: Actions are always cloned. - Action's dstor needs to be public as we have a clone() function. - ActionRegistrys' (and AQ's) getActionByName now returns const ref. We must not return a ptr as it may not get deleted elsewhere. We are handing out prototypes. - queueAction(action*,...) is private to prevent leakage, queueAction(string, ...) is the public interface. - some other small functions are now private, too. - MakroActions now need to clone() the prototype on prepare() and delete them on unprepare(). - ActionSequence deletes contained actions. - FIX: ActionSequenceUnitTest cannot check on not-called property of removed actions anymore as these are gone now (they are deleted on removal and they are cloned on insertion). - DOCU: Updated documentation on Actions. commit 5cf61b4ade7303b1c221599fb66ee1076c5c305e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 3 11:20:16 2015 +0200 Action::isActive() is now const member function. - also changed TextMenu's items. commit 725a1da23441218ebfe802d5508feedc1a4a8b46 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 19:09:47 2015 +0200 FIX: Adjacency's operator<<() printed fixed number (3) of entries. - this caused seg violations and occurred through memcheck run. - it was a copy&paste error from trianglematcher's. commit 3532b77102b83baecdd39fade5a59f5aaf230ed0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 12:21:56 2015 +0200 DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not bin_... - as such they are not installed and hence .in files must not use AUTOTEST_PATH but topdir (top build directory). - also in GuiChecks, regresssion, and Tesselations tests TESTSUITE was made dependent on them but target check and installcheck only actually depend on the wrapper scripts (molecuilder, ...). commit 8e790ebd981dac78daa03f5e06560ba8ea84a21a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 11:27:06 2015 +0200 DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am. ----------------------------------------------------------------------- hooks/post-receive --

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