- Molecuilder-devel

[SCM] branch Fixing_MolecuilderGui created. v1.4.10-63-g8cd4341
by git＠ins.uni-bonn.de 24 Jun '15

24 Jun '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, Fixing_MolecuilderGui has been created at 8cd434159764699e9aa7b69302b9835339eee8f4 (commit) - Log ----------------------------------------------------------------- commit 8cd434159764699e9aa7b69302b9835339eee8f4 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 64c10c32beb00befda40da4e9d54a623bb5bb90f 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 76d35758983956624b2c1a3db3ccf0eaa43bb2c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 17:59:56 2015 +0200 FIX: Neither World nor MoleculeListClass do 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 --

1 0

[SCM] branch GUIStates_using_ObservedValue created. v1.4.10-132-g75364b6
by git＠ins.uni-bonn.de 24 Jun '15

24 Jun '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, GUIStates_using_ObservedValue has been created at 75364b686379f02ac5e498e654e0795023f18760 (commit) - Log ----------------------------------------------------------------- commit 75364b686379f02ac5e498e654e0795023f18760 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 16:22:02 2015 +0200 tempcommit: Fix to _molecule. commit 2410be1fa9782611b278ab9942ee59a2b1ce2873 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 15:37:56 2015 +0200 tempcommit: Fix to GLWorldView, forget to remove connect statement. commit 5cfa4ab44f1d295de9828752fc068b3eb150a81e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 15:36:37 2015 +0200 GLMoleculeObject_molecule also allows for changing molecule's index. - GLWorldScene has new slot changeMoleculeId(), similarly to GLMoleculeObject_molecule's changeAtomId(). commit 9dd7471d60d45f92ddeeeec69ed6b9438a6f6ba0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 15:36:03 2015 +0200 tempcommit: Fixes to _bond. commit e9df649b4dc60c66eff7926f013d60662886f58f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 15:35:39 2015 +0200 tempcommit: Fixes to _atom. commit 501c783fd89f5449a215c563e3ecad374635c344 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 e40bc0b3ef2de970bd77a644850e0ab75ee40f26 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit 3398eeaea723e5f23b899d49c8f38b7c25920484 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit 87bf4b017499c8fb4b4dae5d5850d61c5ecae85c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:15:56 2015 +0200 tempcommit: Changes to _bond. commit 5a226170ae06409be3dfb3f676fdc81c7072c3d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:15:44 2015 +0200 tempcommit: Changes to _atom commit ceb7eaf8398ff03223b7d31cfeedd36625a79bee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:15:21 2015 +0200 tempcommit: Changes to QtMoleculeItem. commit 15116102d2a378e82c6953aa5dbd354ebaf6dac0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 06:49:13 2015 +0200 QtMoleculeItem_... use ObservedValue for internally representing atom's state. - this affects atomcount, formula, and name. visibility depends on clicked state and occurrence is changed elsewhere. commit 32786c5d94ac8ebaa0c1343df23406b0a1d41ef7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit 3e35890170299753563813b8ece39731d08bc9ad 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 14124a72c8f2dde5a0b6f11a8e7846e64d8dd06e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jun 20 02:40:43 2015 +0200 tempcommit: Fixe to trianglematcherin in GuiChecks. Merge with ... commit 177cd5d8acc620f79ea4ee15c566597679b3613a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 19:37:50 2015 +0200 GLMoleculeObject_atom uses ObservedValue for internally representing atom's state. commit 2236c48da4587d6a348761a17505bc7aa817e990 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 623bcb1f9132d9ba0eb2455152954b5fe13b5333 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 19:37:05 2015 +0200 tempcommit: trianglematcher also used in GuiChecks. Merge with ... commit 808f306013fb312d950ed58d870d4ca2d13486fc 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 c68bd8c4827d4380ef9dabd63c840a2baadabd11 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 13:51:08 2015 +0200 tempcommit: Added molecuilderguitest to testsuite dependencies. commit 336814126baeb79fb92853d81a593c0008feb935 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 be7af04f282e3df004fb1dcf84edfcfe0cca851b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 11:32:31 2015 +0200 tempcommit: QtElementList fixes. commit ebf349fcecd354b4743ee6afbde824fb61439c93 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:53:26 2015 +0200 tempcommit: Trying to fix MakroAction's outputAsPython(). commit 7b9cb7c6ef0864811496d7556cdbd5bfe29c2d34 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 82f55be7db82e14ea5003cd699aae3efd0fbecef 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 e69c446f97c5f2264235dbcb04a0ed8ff90c681e 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 d8817de17af7bdeec6d29b050755e82c16d062b9 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 2ea6398a0c7e0f824bccb50acfd6c469e7c6cb8b 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 42ca24539427a0df1e16f3d9056bbe0e371766c3 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 5acaee28c74e200aaa11bce984b3a58892019c2d 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 e6f9daaf049ccc62152eee423dbb2fe39ab07c15 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 55897f55f9c8eb402aa2cad4748a214a1be92e03 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 d750f9ca2d9d9d8dd90fc8712f62a9fad9e47421 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 a9aaa9fa45883d2588e2eb520aafa5b4d093baa9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:23:10 2015 +0200 tempcommit: Fixes to GLWorldScene/View w.r.t. MoleculeMissedStateMap. commit c6c3d202875b7b91e9846cb5bb142f8474e83a2c 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 d1241a84f58c89a92d65ec372692a9d1ebfd5ecb 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 eb87a44364f1c58010634d4325a07c9c25dd68cd 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 988c787c883c5184f305c9fd492347c6d75ca166 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 1009de2c02cb28ccc60406f38e59f3228fa83cfb 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 938d2741d92c9aa35323d4376311541b94610a4f 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 50baad1ef1a40b8e3f40807920ad2e8ce27e5ed5 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 5397d9e586abce51a4da3f4072fe07a8380f587f 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 95d39ebf0ff53b32fee0f09c3a5a9216020ba38e 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 568df3abb720d6fd5586317005e8e8ff702424fd 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 f5f2cbbc2a3e492cc8e276ce80c146cc218be402 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 ef24213beb39fec4c3093ecc8c8f90d18837615d 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 ee6636f10f556951bce74fd93be9816d5ab02b70 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 d619fb42140095bd77e8922aa48840a4dfeb3d7a 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 004956992457b92f9eb2138bb0c261c8252c614d 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 09b198f8c3961b48c7e2da012539d5e375caf448 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 be07501b238c0001b883faad00e456c984bc8dfe 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 bfab8cdbdebae3e1f19201c7cf006ec77d9c8ff8 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 4df3e041dd475cf188ebfe959de58ae1cf339c24 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:13:27 2015 +0200 tempcommit: World::getSelectedMolecules() changes hiccup. - why did this actually change? commit 2d452371d4c6ea7e9f173b633aecd0f7dea79f09 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:01:31 2015 +0200 tempcommit: Change associated to TremoloParser. commit ff227812c319df2a68cebff77ca3a30c91006edd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:01:08 2015 +0200 tempcommit: More ConstAtomComposite hiccup. commit dc3c74999aa6d536deec0801950487af6406ef58 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:54:36 2015 +0200 tempcommit: PdbParser change hiccup. commit d4f2d600952480ea78371e6cb70c002f2ebbd188 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:54:23 2015 +0200 tempcommit: Value_atom changes hiccups. commit 743123116d5f96ab5d765f8236e8b4a0815df178 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:54:07 2015 +0200 tempcommit: ConstAtomComposite change hiccups. commit 8794eb8147db17c46f1166768e8c5b9531ffea7e 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 6d62faac63cc9c12fbfb945eae60933d6eece2cb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:14:10 2015 +0200 tempcommit: AtomIdSet changes hiccup. commit c1d27ffc8b4ddf42e5a64df590ad9973d1dc7ab5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:53:40 2015 +0200 tempcommit: molecule::const_iterator problems (due to FromIdToConstAtom). commit c63553f8ee6372f6a110ea8bc29cf3869982f043 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 10:20:24 2015 +0200 tempcommit: Changes due to molecule::const_iterator (FromAtomToId). commit 3246e73829c6d7b1cd8be824094bd6672e31e5c9 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 02aa4691c99cd62a240d4894f577781015bcfbf4 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 28f4dfb5c9024f2a3636ecdd0fb36beaedaaf355 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 10:20:59 2015 +0200 tempcommit: Changes due to const atom::getMolecule(). commit 2902cb44427b977cd9c13f1e63db5c781159b7d8 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 75ed1736c4851cda5e1cc76a20b76dd448f59684 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 a98e8851aa93546be7523c3f809b0a4961758152 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 5b5759db0e40c1195bf4edbd4e6785e016cbdf44 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 52fe9b5dc5e6d61b562fef9173d0f36f3508c733 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 888aeaf77fc02915e74e3a5d7b4665dc41ff9080 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 fe380db1f83b7f01c50f99bb11e26ad655e287e7 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 5d329da8ae726a361331d42676201803ec25f7fc 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 a15f778c88c4281ef19809961831866b52082ac4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 17:59:56 2015 +0200 FIX: Neither World nor MoleculeListClass do not sign on to molecule changes. commit 88a5527c3477146c7d6484481e3f9e0686ddcd85 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 3aebefb0c61597eb24f2d9ebd90cdfd2eda6c4be 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 b7a98838af4c0d95a103210f033ae0e8e39be431 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 e090e83b073ff14293ffb5b5087ebe39c1ef52c9 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 9496f81208bac10da06f74cc8b30276fc05d4d69 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 22:56:40 2015 +0200 Fixed ObserverLog message in GLWorldView. commit 7e8ffd3ec3cd5fb1839cc8d05eae6e1db33acf11 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 95b53d67ef9d958641335a62e364c8f8da6225d5 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 17556af46363f62fe2726d83e74807532897dd68 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 decc6255d96b42a91c81a215640178ca41fe0400 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 4a67f0f5ce8cc9ecd55a6f1a00a4c816fc007ddf 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 4af30a01bc258772ee450427210b23449468a224 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 abcddcc256bdfacce2d562ae00d49371764e3b58 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 509feca10513e95acde1f09e84666eae6ab9fbc4 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. commit 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 21:23:35 2015 +0200 Set version to 1.4.11. - MoleCuilder library is now 14:3:1. - Codename "Soccer" (It is one for all and all for one football). ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch Candidate_v1.4.11 created. v1.4.10-47-g2fc697b
by git＠ins.uni-bonn.de 23 Jun '15

23 Jun '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_v1.4.11 has been created at 2fc697b743f39b710d3866f7ce2c17542470e39f (commit) - Log ----------------------------------------------------------------- commit 2fc697b743f39b710d3866f7ce2c17542470e39f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 21:23:35 2015 +0200 Set version to 1.4.11. - MoleCuilder library is now 14:3:1. - Codename "Soccer" (It is one for all and all for one football). commit d8255bbda7b87bfebfa457e976bada1578123c45 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 18:48:29 2015 +0200 FIX: ActionQueue would not set LastActionOk to false on general exception. commit dbfb03a85551f15ae02eedfa06c4440bc0aea8ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 15 19:05:37 2015 +0200 FIX: QtUIFactory used executePythonScript without HAVE_PYTHON brackets. commit 3fa16b482f696edb18618700ef768e366d06813c Merge: 08d042d 19dfdf7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 12 15:27:22 2015 +0200 Merge branch 'GUI_niceties' into Candidate_v1.4.11 ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch Candidate_v1.4.11 deleted. v1.4.10-45-g8a83d57
by git＠ins.uni-bonn.de 23 Jun '15

23 Jun '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_v1.4.11 has been deleted was 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f - Log ----------------------------------------------------------------- 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f Set version to 1.4.11. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch SeparatingOutQtThreads created. v1.4.10-151-g0312e23
by git＠ins.uni-bonn.de 18 Jun '15

18 Jun '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, SeparatingOutQtThreads has been created at 0312e2354381e345b8509d9898560703d82ee90a (commit) - Log ----------------------------------------------------------------- commit 0312e2354381e345b8509d9898560703d82ee90a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:58:12 2015 +0200 tempcommit: Fixes to ActionQueue. Merge with 85d6396e commit 9c9df11556737d29a82e1a1277f89b90b17db9fb 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 81e16f2e4caa917357195e371372440b06cda3ce Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:53:26 2015 +0200 tempcommit: Trying to fix MakroAction's outputAsPython(). commit 70a5d45f6149e0e84a6c006a2fb596ecf38ee02c 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 9b45d73a2d2248ad6809d20dd26fc517d8958b36 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 16e19e268e1ad1704eddd2bdda78ed2495a76d9d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 03:23:10 2015 +0200 tempcommit: Fixes to GLWorldScene/View w.r.t. MoleculeMissedStateMap. commit 85d6396e8fcb865db8682c30f6f784751c40112b 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 a986e0aade340029e655abfb95199d2d855562e0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 02:43:15 2015 +0200 tempcommit: QtTimeLine needs DirectConnection. commit 1e1ca86824b1a12b7e16bb8dbb2a5de3dc24e543 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 ef2088a6433ebb723bdda9b3ccf6cc88be54def3 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. commit f39bd7b352b67634c1bd5e2dc6e9bb808cfb7156 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 1a5c53c499d6fa4717a6efe302e3a3e283bd2342 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 01:40:40 2015 +0200 tempcommit: THREAD_BOUNCER change commit da26034e22ef024e4f92421bcfc79d8a5b5c86b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 01:40:23 2015 +0200 tempcommit: Changes to QDebugStream, to no avail. commit a19377e652d285ebcfd83e10a501c470a7907af5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 01:40:06 2015 +0200 tempcommit: Changes to QtMoleculeList mutex usage. commit 88c7eb48d0c3d1517234b97cafd7cb1e773e295d 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 b812fcf938a98a6c8e66717f9bb58b3709dcfc7b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:09:45 2015 +0200 cleanUp() overwrites threadid as there we trigger lots of Observables. commit 2f860f8500be2daab4a5d3695b0f2a7ccdaf96a8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:09:25 2015 +0200 tempcommit: QtHomologyList::needsRefill() uses QueuedConnection. commit eec6fd48ce5a64813dca05f78029bbc4accd800a 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 5950531d074e0a39394fddbe9343df656c012159 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:08:27 2015 +0200 tempcommit: GLWorldScene and View use DirectConnection for acting on inserted molecules. - this should let this signal pass through right away with little delay. commit 6b62ab6eae7b3bb0833c4e36d0e2bd169a3023ca Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:07:56 2015 +0200 tempcommit: QTUIFactory::testrun() waits till UI is done initializing. commit 6c8da4f23ba9d5622fdb91c093248e581fda7201 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:07:40 2015 +0200 tempcommit: Fix to THREAD_BOUNCEr. commit 69cec0aea0fa1a1116386518fadb77df2e820b32 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jun 18 00:06:29 2015 +0200 tempcommit: Fixes to QtMoleculeItem. - all QtMoleculeItems signOn to molecule::AboutToBeRemoved. - getMolecule() may return NULL, is caught at two places. - getMoleculeId() for allowing QtMoleculeList to acess molid. commit 3343be024125ac82ba567222c3e68a1237e90ced Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 23:35:20 2015 +0200 FIX: QtMoleculeItem did not access getMolecule() from World as const. - this triggered an update in the World. commit 64dcb92dab022c3a8678f0b235a487ccfd65b7f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 23:35:04 2015 +0200 tempcommit: Deactivated THREAD_BOUNDER, only .._VIP active. commit 7efd69375a557e74b040101627716da68741e4f7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 23:34:46 2015 +0200 tempcommit: Further THREAD_BOUNcER fixes. commit 45736c64442252050628d0e5bb5fa61273c56694 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 23:33:30 2015 +0200 tempcommit: FIX: QDebugStream is now thread-safe. Merge with <QTextCursor registering> - also Fix to QTextCursor not registered. commit 2cda9e5eccd4912ab2e57624bbee9188526eb183 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 23:21:42 2015 +0200 tempcommit: Fixing ObservedMolecules complaining about missing molecule. Merge with ... - we get one subjectKilled per channel! commit 3f3feb76057456c7372a4bf14a5494cebfdbd00d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 20:32:37 2015 +0200 DROPME: Added THREAD_BOUNDER and .._VIP everywhere. commit 4ce6318731c8aebedd419f362437b0c3e9ae19ea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 20:10:59 2015 +0200 tempcommit: Merge with f2129a4 commit 6e278aa9d97103a742a70671dbd9c3b4167cc661 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 19:27:25 2015 +0200 Added ThreadGuard include in every Qt module. commit f2129a4044e7428a570f6dcb83de4a72fde459f3 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 0708ac1c1694fdb01b4060dd01c069080333c0f5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 19:02:27 2015 +0200 FIX: GLWorldView::recieveNotification() is checking for whether molecule actually exists still. commit 20173d899dfe873ab99c679f30a5aedf403d945b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 19:01:51 2015 +0200 DROPME: Making sense out of why subjectKilled goes to wrong observer. commit ab3323811e53c46d541bf31b43d63aeb735eee64 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 61f6eb3f850e9ee1e78df1896f5a67246e98860b 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 497876e9730b36a0844b68e26cfd0eb342e55171 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 634622679668fadca2d997160aaf00da82e9f754 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 17 18:58:32 2015 +0200 tempcommit: Attempt at fixing QTextCursor not registered error. commit c1a3fdc492d04cde685082208acb969a0e3a0dcc 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 fb3ff0d970b1edbf90b1ad9e3c3d4681040ce519 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 15 23:01:44 2015 +0200 tempcommit: Taking note of subscribed molecules to sign Off on GLWorldView's destruct. commit 750e6bfb879681b62fe1c092d7bf7fde04f28c54 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 15 23:01:19 2015 +0200 tempcommit: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted. commit 00a4670cf6c8929ac6da73af4ceb29aea78aa41f 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. commit 78d5dad6dfbcae9f1f8be551956919aad589597e 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 f6efee1791b105055db281150be732dcaff08464 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 8 18:27:25 2015 +0200 tempcommit: Merge with 9e859c19 commit 04a74e50838356c9bbdb18c94de78610452c7442 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. commit 6eabab62aaeb92f03ecf56bc34206e2fd3a30462 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 19:19:49 2015 +0200 Revert "tempcommit: Attempt on fixing the asynchronous handling of signal/slot and observer/observable systems in GLMoleculeObject_molecule." This reverts commit 5888dcffe918e3788a2e25fe116597943cff6cec. commit 5888dcffe918e3788a2e25fe116597943cff6cec Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 19:11:51 2015 +0200 tempcommit: Attempt on fixing the asynchronous handling of signal/slot and observer/observable systems in GLMoleculeObject_molecule. commit df9b6859b1d0b312539d3fae9d5402640d31bb14 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 16006dbeb16f74c42c8d29d8ba6497af7bfc1282 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 f302731d0890e3dee562d9972a71a32f3470cedb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 14:54:00 2015 +0200 Revert "FIX: GLMoleculeObject_molecule::init() is now a slot." This reverts commit 11313115aa28c8de65d26aa5cba377547126f6b5. commit b4bfa7037399a6e7be88c8c983b57873c23fadb5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 14:53:38 2015 +0200 tempcommit: Merge with 8acec5c6 commit f1162b71de76b98015a439aa6a92db7774a52580 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 14:45:20 2015 +0200 tempcommit: QtElementList does not have a changed() signal. Merge with ... commit 11313115aa28c8de65d26aa5cba377547126f6b5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 14:44:22 2015 +0200 FIX: GLMoleculeObject_molecule::init() is now a slot. - this should fix non-causality of signal/slot with observer-related signals, i.e. atomRemoved may get in before the atom has been instantiated within init(). commit d2a3e6168da7375b33b28c6c9d1cc1e4a700ac32 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 3a852aefbeca35371e57a6c1bcd4c569e01d7adf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 13:23:24 2015 +0200 tempcommit: Merge with 8acec5c6 commit 95e7efa17499e5c2fd508f0052e35890112385dc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jun 2 12:43:49 2015 +0200 tempcommit: molecule's Formula is not changed when atom changes element. commit 8acec5c66a90d043870fea994a212285bf1153af 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 f82b1b9c5919a6428a0ada2e891e5a3220cc77f5 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 6308b5c267220cd45e610b5d5f98a8c3c727bae1 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 e425c3f8e807861c3ff09b9bde415c9ad6deab81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:14:10 2015 +0200 tempcommit: AtomIdSet changes hiccup. commit 4517da28262baee58762721a801aa598498e4884 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:13:27 2015 +0200 tempcommit: World::getSelectedMolecules() changes hiccup. - why did this actually change? commit e973bf4445d3cfe90893f0191eb601beb39b1fae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:13:04 2015 +0200 tempcommit: ParserXyZUnitTest hiccup. commit 04cd84a317a6a256f270906b4e3eb423a14e9444 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:01:53 2015 +0200 tempcommit: MoleculeDescriptorUnitTest hiccup. commit a1777369e1ab75c4d5c05e128dbd722a80d20e72 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:01:31 2015 +0200 tempcommit: Change associated to TremoloParser. commit 310a571cdd564f17170ff98a6667b8f723b460e7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 22:01:08 2015 +0200 tempcommit: More ConstAtomComposite hiccup. commit 6357a7781590d2a371a8e839caf53da98a880056 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:55:38 2015 +0200 tempcommit: Forgot Makefile.am change in AtomNameDescriptor adding. commit be9f02462ecccd27bc5ae8a5143c1d23eb63e029 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:54:36 2015 +0200 tempcommit: PdbParser change hiccup. commit 8d69856c8f974617deef515ad8b0dcdbc80dd458 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:54:23 2015 +0200 tempcommit: Value_atom changes hiccups. commit ffdc50797acf2e252d63930d6c79568d3369b423 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:54:07 2015 +0200 tempcommit: ConstAtomComposite change hiccups. commit 6221a31dc4c1159fa8263a27cfe8e537d0b5287d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:53:40 2015 +0200 tempcommit: molecule::const_iterator problems (due to FromIdToConstAtom). commit 6a3ca760b4092aa67b57ffe88f745eff843fd5db Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:23:21 2015 +0200 tempcommit: Probably due to changes to get..Molecule..() commit 111c4b44ee95848dfcca88188fcbfbf19c4894a6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 21:16:32 2015 +0200 tempcommit: Merge possibly with 20f88fee commit ed3a55ff2e70dc044ae10fb3c9954620430b5d6f 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 30e530076bcc6a5a2f000648b93d15970c7ba78d 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 20f88fee951e0f0975e03dab347bb29f38bb8832 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 565777c816ad145911eda994458c07fa9adb3ea3 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 f73a348113c0d657d8f53d1d478e30555dfaf4cc 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 c8320fe241f4c1c68f30b7b1fbcc521bee3060d6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jun 1 09:42:19 2015 +0200 tempcommit: DOCU: Corrected userguide. - this still needs some more work, e.g. w.r.t to code snippets indentation. commit 5dabe20d14db77a7f638c6fce075e81d038cc2aa 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 daadba6cd9e872a5628db5a17075fd72a6960fe0 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 0c326f15463110db89fdf2110b2aaafc868e5faa 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 2054e6b36d8608258d6d67b0a929c6ab2aaf41e8 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 200da30b5cbf895becc7c8b64685706c7a729fbf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 31 17:59:56 2015 +0200 FIX: Neither World nor MoleculeListClass do not sign on to molecule changes. commit 4fee79b8c5ecdb10388059db8ed19fe83f2a5ba7 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. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch MolecuilderGuiTestSuite created. v1.4.10-39-g08d042d
by git＠ins.uni-bonn.de 12 Jun '15

12 Jun '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, MolecuilderGuiTestSuite has been created at 08d042d999587b9169fbb5763d93a65241a1cf4f (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch MolecuilderGuiTestSuite deleted. v1.4.10-39-g80b555f
by git＠ins.uni-bonn.de 12 Jun '15

12 Jun '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, MolecuilderGuiTestSuite has been deleted was 80b555f2762e4c07533b77c414b36bce168fb47e - Log ----------------------------------------------------------------- 80b555f2762e4c07533b77c414b36bce168fb47e Added "--testsingle" switch for line-by-line execution. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch Candidate_v1.4.11 created. v1.4.10-45-g8a83d57
by git＠ins.uni-bonn.de 12 Jun '15

12 Jun '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_v1.4.11 has been created at 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f (commit) - Log ----------------------------------------------------------------- commit 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 21:23:35 2015 +0200 Set version to 1.4.11. - MoleCuilder library is now 14:3:1. - Codename "Soccer" (It is one for all and all for one football). commit 3fa16b482f696edb18618700ef768e366d06813c Merge: 08d042d 19dfdf7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 12 15:27:22 2015 +0200 Merge branch 'GUI_niceties' into Candidate_v1.4.11 commit 08d042d999587b9169fbb5763d93a65241a1cf4f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:34:31 2015 +0200 Added "--testsingle" switch for line-by-line execution. - QTUIFactory checks for additional "single" and activates then a special mode which uses the newly split executePythonScript. commit 37a67f216a1ec48288bc1b314c99cfb0d6cb6963 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 15:50:53 2015 +0200 Replaced Query.. class and query..() function declarations in Dialog.. by boost preprocessor magic. - this removes a lot of copy&paste code. commit 0435989b70a2b793f218705f1cf498471af2bdd2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:24:19 2015 +0200 Replaced all std::string by ParameterPair where used as ("key = value;") tuples. - this fixes an issue with vectors of key-value-pairs converted into a single string for use in a python command. commit 33e80133683ce15eb991faac6abc6d540afee182 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:22:43 2015 +0200 Added ParameterPair (i.e. "key = value;") to allow other string output. - this will solve the problem of vectors of key-value-pairs not properly converted into a single string because of missing semicolon. - FIX: toCLIString used functions toPythonString if possible. commit dd6c07d2c5d563c8e46c0a4b01a0de11563eb584 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:22:40 2015 +0200 Added all new guichecks regression tests generated from createGuiChecks.sh script. commit fae462dafc0b0506501581e2bccedaef6813450d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:03:03 2015 +0200 Added script file to generate guichecks testsuite from regression tests. - options-no-elements.db and options-empty-configs works with faulty arguments. This cannot be replicated with molecuildergui. - all load- and store-sessions removed due to (then) multiply occurrences of said action (we need store-session to create the script for molecuildergui). - dry-run will not cause errors, hence error code of script creation call must always be 0. - refreshes TESTSCRIPTS variable in Makefile.am. commit f3db6059ff3cc60a56408536bc8c419fc809da01 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 09:12:44 2015 +0200 Added DryRun and NoDryRun actions. - actions (un)set a flag inside ActionQueue to which only those permitted by an advocate pattern have access. - added testsuite tests for both dry-run, no-dry-run, and storing sessions. - explained use of action in userguide. commit 0907ad2590d5fe8b17e1ee653a60c21f3b4e11d0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:24:48 2015 +0200 Added GuiCheck "AddAtoms". commit 0f0407ad8f57ba8adda5a1059fe7125b8aaa5b92 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 21:49:52 2015 +0200 Added testsuite "GuiChecks" with extra target guicheck. - this allows starting the testsuite on the graphical interface. - checks for working testlauncher inside molecuildergui with single and multiple scripts. commit 15e1978cca9c4568b8ac921a0fee1cac72517d81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:20:52 2015 +0200 Command-line arguments are passed to QApplication inside QtUIFactory. commit 3054689a58736f5438fa03886a4337356078607b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:17:55 2015 +0200 Added "--test"-mode to UI switch in builder_init. - this will allow to launch molecuildergui with a set of scripts to execute. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch DebianPackaging created. v1.4.10-73-g391923a
by git＠ins.uni-bonn.de 23 May '15

23 May '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, DebianPackaging has been created at 391923ab6c70fce7fc420886301c9b8a1bc0be4d (commit) - Log ----------------------------------------------------------------- commit 391923ab6c70fce7fc420886301c9b8a1bc0be4d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 21:04:44 2015 +0200 Added script for creating debian package. commit 24fcd78d341029266bd5f4b46b4a4ab5c2c2ff9a Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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 d3973c60b7192a8574be94bb9e6a7ab7c9312f43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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 984dc8b16b3ffb3e87c4c6a4947c84321771f075 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 20:32:01 2015 +0200 DOCU: Described workaround for missing pyconfig.h. commit ff8b451ef1bac854932f1dfb2f405a37cecb2c6d Author: Frederik Heber <heber(a)ins.uni-bonn.de> 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). commit 9ae0efcc83c4d1210debe2172c0c02d3e213c017 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 8382df968502806eb6c61502c1be4fdd2b7d14cc 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 6c67992de3e984db28a78310cd2de095102d95b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 23:06:19 2015 +0200 tempcommit: regression test maxiter, grep was wrong. Merge with ... commit 93c2b7a091036201ebb6d0abc7b09633768c4453 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 de8bd76963bd40c0c20d7ace5c335fa40c907890 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 22:56:40 2015 +0200 Fixed ObserverLog message in GLWorldView. commit b6936a533fd2409fd9fd349b7e9d74df6c4502a8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 21:25:21 2015 +0200 tempcommit: Merge with 76f50540 commit 6cb4919bd3771a9bae21d92ef1452f3f3395c685 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 21:02:57 2015 +0200 tempcommit: createGuiChecks refreshes TESTSCRIPTS variable in Makefile.am. commit dc984aa919e1cda66a23e3fe30e524c16eca8023 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 21:02:45 2015 +0200 tempcommit: Merge with ffcce10e70 commit 12c5aa359a91b1fb76135d41398901c40916566a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 21:02:13 2015 +0200 tempcommit: Modified all scripts to call molecuilderguitest. Merge with ... commit ffcce10e70aa0fb143d466aa9a461d5db6a09c83 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 4b1e0af0dbe2c4b854d4310557826c839bd898d8 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 e2afd36f264edd243bc4f9a217c2724ba16593a8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:15:17 2015 +0200 tempcommit: Removed guicheck's Makefile.in again. Merge with ... commit 28c0b20a98eb22f6d7ce2395a8e6a00f57721822 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:10:49 2015 +0200 tempcommit: Renamed molecuildergui -> molecuilderguitest. - also added "--test-single" to molecuildergui call. commit 10082714bdae5d6b38dbb3e9e87d96d57e18670d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 20:08:35 2015 +0200 tempcommit: Forgot to add guicheck's moleculder..in to Makefile.am. Merge with ... commit a38f29ba04abb349e9026e88cd6cd5bb07f58818 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 c64b132c1eb7b7fc6c4b653a0a80abac28e0f033 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 76f50540022c3b42aa944b3bb070a67e959b72a5 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 a9bd0484f2d75db5ff716a35ddf191221cfa9119 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 20 19:26:12 2015 +0200 tempcommit: exit code is set at end of main() not by QApplication::exit(). Merge with fdc9163a commit 2cc6dd8c84b848f354f78cbf195c6e8ccb27db1e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue May 19 07:29:30 2015 +0200 tempcommit: regression test set-parameters-mpqc had too many white spaces. commit fdc9163a968c83b1fcd11b1decb68e1a1ffe050c 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 7d1b9cb3b4a862eea4bed34d9e2a85c57a360f31 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon May 18 19:25:51 2015 +0200 tempcommit: GuiChecks updated and several files excluded. - options-no-elements.db and options-empty-configs works with faulty arguments. This cannot be replicated with molecuildergui. - all load- and store-sessions removed due to (then) multiply occurrences of said action (we need store-session to create the script for molecuildergui). - dry-run will not cause errors, hence error code of script creation call must always be 0. commit c83704790cd63baa4cbf062d5713e656a72fe316 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 19:49:55 2015 +0200 FIX: regression test Save Bonds used direct molid of 0. - this might break things in guichecks, using last molid "-1" rather. commit ab329a3a40e30ece93315c822657608ab37bae42 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 5466c027b94e0250fdd2b45327250fe32571acca 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. commit 4381f2915ea08cdf2cebb64cbda7dfe24ad9f722 Merge: 0e215c4 19dfdf7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue May 19 10:36:40 2015 +0200 Merge branch 'GUI_niceties' into Candidate_v1.4.11 commit 0e215c4b11e0d5bf05ea02a0d21751df53df7164 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:34:31 2015 +0200 Added "--testsingle" switch for line-by-line execution. - QTUIFactory checks for additional "single" and activates then a special mode which uses the newly split executePythonScript. commit df465515851aceb1eaaee1ccf579c7fc9497fa3e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 15:50:53 2015 +0200 Replaced Query.. class and query..() function declarations in Dialog.. by boost preprocessor magic. - this removes a lot of copy&paste code. commit c57e955b7fe9d9590fa5a00d73cda68a161a70aa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:24:19 2015 +0200 Replaced all std::string by ParameterPair where used as ("key = value;") tuples. - this fixes an issue with vectors of key-value-pairs converted into a single string for use in a python command. commit 9e79aceda2881e5c92afd7a73369cc7e7f0a43ee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:22:43 2015 +0200 Added ParameterPair (i.e. "key = value;") to allow other string output. - this will solve the problem of vectors of key-value-pairs not properly converted into a single string because of missing semicolon. - FIX: toCLIString used functions toPythonString if possible. commit 882f7c73301d81c9d7e7104661a94432a7724bf0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:22:40 2015 +0200 Added all new guichecks regression tests generated from createGuiChecks.sh script. commit 58798be154020b7ca815a9af55d86bea35036861 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:03:03 2015 +0200 Added script file to generate guichecks testsuite from regression tests. commit abb9b3569975869402de407eb187cda8073f196c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 09:12:44 2015 +0200 Added DryRun and NoDryRun actions. - actions (un)set a flag inside ActionQueue to which only those permitted by an advocate pattern have access. - added testsuite tests for both dry-run, no-dry-run, and storing sessions. - explained use of action in userguide. commit 19dfdf7a57ea6922cc8f70fc0fcfc9892599fb26 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 15:41:21 2014 +0200 Increased timer interval in QtStatusBar to 4secs. commit 503a7fd9b90c9c871ec1e80dea6741c91ba86625 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 8 13:05:08 2015 +0100 FIX: QtMoleculeList hiccup'ed on update-molecules for two water molecules. - the problem is that readdItems() adds the group item that is later gonna be removed anyway and hence causes a segfault in the next update. This is fixed. commit 5dcb3c5962bb64ba0c108d3eb380e55e5dea7dc6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 8 12:59:48 2015 +0100 QtInfoBox shows Atom's position components separately and molecule's center. - single vector is hardly readible because infobox is very slim. - increased minimum height of QtInfoBox a bit to have all values showing. commit b8463f9359f589186af2a8ff5c8cd1b7e2510ed9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 8 12:19:55 2015 +0100 FIX: RotateAroundSelf converted rotation angle to rad in params. - this caused wrong angles written in StoreSession (in radian and not in degree as expected). This fixes ticket #251. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch MolecuilderGuiTestSuite created. v1.4.10-39-g80b555f
by git＠ins.uni-bonn.de 18 May '15

18 May '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, MolecuilderGuiTestSuite has been created at 80b555f2762e4c07533b77c414b36bce168fb47e (commit) - Log ----------------------------------------------------------------- commit 80b555f2762e4c07533b77c414b36bce168fb47e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:34:31 2015 +0200 Added "--testsingle" switch for line-by-line execution. - QTUIFactory checks for additional "single" and activates then a special mode which uses the newly split executePythonScript. commit c9fef24982e7e05c4f4b6444d0f20ef211936f03 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 15:50:53 2015 +0200 Replaced Query.. class and query..() function declarations in Dialog.. by boost preprocessor magic. - this removes a lot of copy&paste code. commit 1d297b737fd450fc9ce02966dbf20385a9975719 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:24:19 2015 +0200 Replaced all std::string by ParameterPair where used as ("key = value;") tuples. - this fixes an issue with vectors of key-value-pairs converted into a single string for use in a python command. commit 1a19cbd03341a0260953a3dd145bfa535cb63e88 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:22:43 2015 +0200 Added ParameterPair (i.e. "key = value;") to allow other string output. - this will solve the problem of vectors of key-value-pairs not properly converted into a single string because of missing semicolon. - FIX: toCLIString used functions toPythonString if possible. commit e6f5d13231ef3b0693eb671880488a3515a8208f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:22:40 2015 +0200 Added all new guichecks regression tests generated from createGuiChecks.sh script. commit 757e619284a27d532b1b9f1ec83dccab0c89da81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 10:03:03 2015 +0200 Added script file to generate guichecks testsuite from regression tests. commit 911f82ab18c501e1f9151c93792a77c5953e769b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 15 09:12:44 2015 +0200 Added DryRun and NoDryRun actions. - actions (un)set a flag inside ActionQueue to which only those permitted by an advocate pattern have access. - added testsuite tests for both dry-run, no-dry-run, and storing sessions. - explained use of action in userguide. commit 83f4c55b05b699762436efee76df292f4ce6813a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:24:48 2015 +0200 Added GuiCheck "AddAtoms". commit 255b3dd02746d2ed63ed4e773c943f72bfae2fcc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 21:49:52 2015 +0200 Added testsuite "GuiChecks" with extra target guicheck. - this allows starting the testsuite on the graphical interface. - checks for working testlauncher inside molecuildergui with single and multiple scripts. commit 341a4ab7727a06ab853a7f4abdb7ab4605b80c4a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:20:52 2015 +0200 Command-line arguments are passed to QApplication inside QtUIFactory. commit 9e859c19297caa27af15119364739184569abe77 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 20:17:55 2015 +0200 Added "--test"-mode to UI switch in builder_init. - this will allow to launch molecuildergui with a set of scripts to execute. commit 3a4be0dfdbe8f8c566c8fc42b0e9a6c0a2bf76b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:02:25 2015 +0200 FIX: Removed specific queries for RandomNumberDistribution_Parameters. - also removed RandomNumberDistribution_ParametersType from TypeEnumContainer. commit 2cf12ab228eeb33e76449aa2ee8e2b1d344cca65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:33:08 2015 +0200 Split executePythonScript into file and string script option. - as python script is internally a string anyway, this allows more freedom in creating or internally modifying python scripts. commit 06993ecb24e553d7fd2081b4d733f40e007e7c65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 09:32:01 2015 +0200 FIX: double inclusion protection used already used name. - PythonScripting instead of PythonScripting_impl. commit 645f55e87502d3647d80248b8a8bcc981c2aa934 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 08:44:58 2015 +0200 FIX: VerboseAction would store invalid undostate (just success). - this is due to switch between whether verbosity actually changes or not. However, we always have to return a full undostate (or just success if no undo can be performed) when undo/redo is implemented. commit 22ac22aca3c37906d62a9c98e92163e0784a003b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun May 17 06:25:29 2015 +0200 FIX: Fastparsing regression test contained one broken line. - this occurred in 2700983e. commit f0cf79849c9d80e77e36a5b95dbd51578f8b1ab3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed May 13 22:06:44 2015 +0200 FIX: Setting window title in QtMainWindow. commit b9b49e727d9d3d89c559b4370e78e73dd898f45d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Feb 6 14:22:15 2015 +0100 createMoleculeMesh now checks that minradius is at least the minimum bond length in the molecule. commit 88afc98ce3204073139972574abd21cf592b7f3a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:25:11 2015 +0100 Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms. - renamed add/remove-bond -> add/remove-bond(s) to emphasize this. - added regression test on three selected atoms. - modified userguide entry for both actions. commit 2fcef36f8dcba275ab6b2280c2ac65fea1f5322a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 22:28:27 2015 +0100 Added SaturateAction that uses SphericalPointDistribution. - added saturate-atoms to userguide. - added regression test fpr saturate-atoms. commit 0241c59e7f10c73f87336715af0aadac2b2d4db1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Trimmed down SphericalPointDistribution to what is needed at the moment. commit f54930fdd572cf1e5e916da920bdad10f75cd695 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 041b77534fcad37539d2dc51316181ca20789d92 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit e895f78dbdbe38b130210c4366e7fed23c4fe47a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. commit f47efd4ebdb376bfe1356fa44faf9dfb3aadcee1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 12:07:22 2015 +0100 FIX: Bond cylinders were wrongly scaled and too long with degree larger than one. - we have to first translate, then rotate, then scale. The last two were interchanged before. This is fixed. commit 605b920d2069e10cd6251ac3594f694e3a77a4aa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 16:33:42 2015 +0100 TESTFIX: Output for target "extracheck" in logs is not helpful if just the log is sent back. - now the resulting energy is stated in the log as well. commit 6a62766a98501b3d23237fd55ecf9e408d515b6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 26 21:26:48 2015 +0100 FIX: MPQCData::DoValenceOnly was wrongly initialized. commit 52dfccf25b899535cbc0c015b9e1f78b9091a02f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 22:19:53 2015 +0100 FIX: QDebugStream is now protected against multiple writes to log window. - writes bracketed with bool. - we had multiple, seemingly random segfaults in QDebugStream when inserting new text. commit b569b869983a53f9cfd8504c35519a4e5d5816ae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 18:37:49 2015 +0100 FIX: MPQCCommandFragmentController failed to add jobs due to false return value type. - bool is now an unsigned int. - kudos to Ralph Thesen und Sambasiva Rao Chinnamsetty for stumbling over the bug. commit ca09be78bbfa6e8031a56eeddb3ea077f2898239 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:51:25 2015 +0100 FIX: FragmentationAutomationAction checks FragmentControllers' exitflags. - this way we can tell when the connection to the server fails and we need to interrupt the Action and return failure. commit c17aa82e3ef91ee1d287c21853069780b7d77509 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:50:27 2015 +0100 FIX: ActionSequence now checks whether an Action in the sequence fails. - otherwise if we are to repeat the sequence for 200 steps and one of the Actions fails on the first step, we still go through all of the remaining steps. commit 0763cebcd4404462360473dcb6a67eb7d3459907 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:31:53 2015 +0100 Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect. - this fixes the bug where the molecular dynamics actions would flip the double bonds in an aromatic ring during the simulation steps because the bond degrees are reset even though the bond graph is present and should be re-used. commit cd5aa0e9ee7d7b9d60b2e207fefdcbdff931dba3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:30:48 2015 +0100 Added correct-bonddegree to MolDyn and StructOpt Actions. - this is not really necessary as FragmentationAction will correct bond degrees but it is nonetheless cleaner this way. commit 329cf3be784f771a68fd139004a418721050fa4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:57:10 2015 +0100 FIX: All MakroActions now have prototype_actions and copy from that. - this fixes the segfault when calling a MakroAction such as MolecularDynamics and unchecking output-every-step, causing the OutputAction to be removed from the sequence, and when re-performing Action with again unchecked option, the action cannot be removed any longer. - prototype_actions is prepared in ActionRegistry on program start and all cloned MakroActions copy their specific actions set and MakroAction accesses it via a ref in callAll(). commit c1d8370d3b839d18339477ec374e2e99aa98c3b7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 10 13:18:33 2015 +0100 FIX: [push/pop][Atom/Molecule]Selection would store ptrs instead of ids. - this is potentially risky as popping a selection may occur at a later stage where the ptrs has been deallocated. Hence, we now store only ids and these get reselected on popping. - also fixed some faulty message with respect to associated Actions. commit c2661740e680214aedbfd198a49ab05ae0eedc43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:37:44 2015 +0100 Undoing atom/molecule removal will also recreate bonds. - TESTFIX: Molecule/Remove Undo had wrong check file (bonds were still missing) commit e23fecd7d546524c9be983551b4b3a1efbdea050 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:34:57 2015 +0100 Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId(). - I just stumbled over this, trying to recreate bonds from removed atoms and Contains looks for the Nr not the Id ... commit 91730001a1c217b3fd68de844f85cfef323e7c5c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 10 10:23:51 2015 +0100 FIX: UndoRedoHelpers' AddBondsFromBondInfo would add bonds doubly. - also, if adding goes wrong, added bonds are now removed again. commit b56114adf8691cb8640747de16866a6c1d22f7da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 20:43:55 2015 +0100 FIX: Action..::outputAsPython now accesses parameters via getUnvalidated(). - added Value::getUnvalidated() and Parameter::getUnvalidated() for access at store-session. - this fixes a bug when OutputAsAction had been used whose filename would no longer be valid as the file now exists. This would cause an assertion and the whole OutputAsAction would fail. ----------------------------------------------------------------------- hooks/post-receive --

1 0