September 2014 - Molecuilder-devel

[SCM] MoleCuilder branch Candidate_v1.4.8 created. v1.4.7-54-g4d966a0
by git＠ins.uni-bonn.de 16 Sep '14

16 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been created at 4d966a045dba17945ab7e6433ebf4faea3d73b17 (commit) - Log ----------------------------------------------------------------- commit 4d966a045dba17945ab7e6433ebf4faea3d73b17 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:06:47 2014 +0200 Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - Codename "" (). commit 06b5dfa95337fee961ce3018c5e56e6b64c06454 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 16 02:09:36 2014 +0200 FIX: CommandLineParser causes idling thread when parsing goes wrong. - CommandLineParser::Parse() now returns bool to give status of parsing, only when true is scanForArguments() called, which fills the ActionQueue's queue which is not executed anymore because the run thread was already stopped by the caught exception from the parse failure. commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 23:29:05 2014 +0200 MEMFIX: Thrown ParserException causes mem leak in LoadAction - also added catching of exception to both LoadAction and InputAction. commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 Merge: b73545e 8859b5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:05:28 2014 +0200 Merge branch 'GUI_Fixes' into stable commit b73545e66c148c8d0fce990a5e3138a99fadcc28 Merge: 55736be 5524ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:28:50 2014 +0200 Merge branch 'MemFixes' into stable Conflicts: src/Tesselation/boundary.cpp - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes. commit 55736be799388502de9a57ac542d215e5ce0565a Merge: 29b35ef 5a9f4c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:22:29 2014 +0200 Merge branch 'Cleanup_old_code' into stable ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 deleted. v1.4.7-54-g586f10c
by git＠ins.uni-bonn.de 16 Sep '14

16 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been deleted was 586f10c83860e32bd4385827fe0c3e97d2ba55cf ----------------------------------------------------------------------- 586f10c83860e32bd4385827fe0c3e97d2ba55cf Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 created. v1.4.7-54-g586f10c
by git＠ins.uni-bonn.de 16 Sep '14

16 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been created at 586f10c83860e32bd4385827fe0c3e97d2ba55cf (commit) - Log ----------------------------------------------------------------- commit 586f10c83860e32bd4385827fe0c3e97d2ba55cf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:06:47 2014 +0200 Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - Codename "" (). commit ddfbd403ac839c27e59df6bc1810504ffec4fa86 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 16 02:09:36 2014 +0200 FIX: CommandLineParser causes idling thread when parsing goes wrong. - CommandLineParser::Parse() now returns bool to give status of parsing, only when true is scanForArguments() called, which fills the ActionQueue's queue which is not executed anymore because the run thread was already stopped by the caught exception from the parse failure. commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 23:29:05 2014 +0200 MEMFIX: Thrown ParserException causes mem leak in LoadAction - also added catching of exception to both LoadAction and InputAction. commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 Merge: b73545e 8859b5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:05:28 2014 +0200 Merge branch 'GUI_Fixes' into stable commit b73545e66c148c8d0fce990a5e3138a99fadcc28 Merge: 55736be 5524ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:28:50 2014 +0200 Merge branch 'MemFixes' into stable Conflicts: src/Tesselation/boundary.cpp - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes. commit 55736be799388502de9a57ac542d215e5ce0565a Merge: 29b35ef 5a9f4c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:22:29 2014 +0200 Merge branch 'Cleanup_old_code' into stable ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 deleted. v1.4.7-53-g05341a0
by git＠ins.uni-bonn.de 16 Sep '14

16 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been deleted was 05341a09115eb72edd1ad3c7350702234bb2fa73 ----------------------------------------------------------------------- 05341a09115eb72edd1ad3c7350702234bb2fa73 Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 created. v1.4.7-53-g05341a0
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been created at 05341a09115eb72edd1ad3c7350702234bb2fa73 (commit) - Log ----------------------------------------------------------------- commit 05341a09115eb72edd1ad3c7350702234bb2fa73 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:06:47 2014 +0200 Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - Codename "" (). commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 23:29:05 2014 +0200 MEMFIX: Thrown ParserException causes mem leak in LoadAction - also added catching of exception to both LoadAction and InputAction. commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 Merge: b73545e 8859b5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:05:28 2014 +0200 Merge branch 'GUI_Fixes' into stable commit b73545e66c148c8d0fce990a5e3138a99fadcc28 Merge: 55736be 5524ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:28:50 2014 +0200 Merge branch 'MemFixes' into stable Conflicts: src/Tesselation/boundary.cpp - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes. commit 55736be799388502de9a57ac542d215e5ce0565a Merge: 29b35ef 5a9f4c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:22:29 2014 +0200 Merge branch 'Cleanup_old_code' into stable ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 deleted. v1.4.7-52-gf07f16f
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been deleted was f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f ----------------------------------------------------------------------- f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 created. v1.4.7-52-gf07f16f
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.8 has been created at f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f (commit) - Log ----------------------------------------------------------------- commit f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:06:47 2014 +0200 Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - Codename "" (). commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 Merge: b73545e 8859b5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:05:28 2014 +0200 Merge branch 'GUI_Fixes' into stable commit b73545e66c148c8d0fce990a5e3138a99fadcc28 Merge: 55736be 5524ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:28:50 2014 +0200 Merge branch 'MemFixes' into stable Conflicts: src/Tesselation/boundary.cpp - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes. commit 55736be799388502de9a57ac542d215e5ce0565a Merge: 29b35ef 5a9f4c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:22:29 2014 +0200 Merge branch 'Cleanup_old_code' into stable ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_Fixes updated. v1.4.7-18-g8859b5e
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

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 "MoleCuilder". The branch, GUI_Fixes has been updated via 8859b5e80aaacf810ed6de2750789019357f0fa0 (commit) via 29b52b1607551f45b84d99fb44f6e5e121221626 (commit) via 9bdcc9b9d75a09f2bb7ddfba50b34f7ad62a7e68 (commit) via 0ac3e3aeb53bc6b57899974dd8ec414158ffaccc (commit) via f8bccc9d2f41fb1866651aadba4beab9fe0bea1d (commit) from 0741f4d175456b6ffd128ea624a7a20273533b6c (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 8859b5e80aaacf810ed6de2750789019357f0fa0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 12 10:00:59 2014 +0200 Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions. commit 29b52b1607551f45b84d99fb44f6e5e121221626 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 12 10:00:16 2014 +0200 Made ActionQueue observable. - has channel ActionQueued. - this is preparatory to know about most used Actions. commit 9bdcc9b9d75a09f2bb7ddfba50b34f7ad62a7e68 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 11 22:55:47 2014 +0200 FIX: QtHomologyList lacked use of FunctionModel::filter_t to split up arguments. - we need to split up the vector of arguments into lists of argument tuples that each potential can digest. And these tuples are different per potential. commit 0ac3e3aeb53bc6b57899974dd8ec414158ffaccc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 11 09:30:53 2014 +0200 FIX: QSeisPlotPage takes up all remaining space in QtHomologyList. - thanks to http://stackoverflow.com/questions/11911323/how-to-allow-a-qwidget-to-expan… commit f8bccc9d2f41fb1866651aadba4beab9fe0bea1d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 11 00:12:17 2014 +0200 FIX: QtQueryList now works with pointers, FileQtQuery gives name of file. - FileQtQuery always said "input-file:" which becomes ambigious when multiple files are queried in a single dialog. - Value_string was a specialization for string type. This was used to also specialize for element type (and also for atom and molecule type). - This automatically fixes problems where QtQueryList would show memory addresses in the list instead of e.g. element names. This occurs because toString() is used on the pointer, now getName() is called. ----------------------------------------------------------------------- Summary of changes: src/Actions/ActionQueue.cpp | 15 ++- src/Actions/ActionQueue.hpp | 29 +++- src/Parameters/Makefile.am | 26 ++- .../Specifics/Value_atom.cpp} | 63 ++++--- src/Parameters/Specifics/Value_atom.hpp | 33 ++++ .../Specifics/Value_element.cpp} | 52 +++--- src/Parameters/Specifics/Value_element.hpp | 33 ++++ src/Parameters/Specifics/Value_molecule.cpp | 76 ++++++++ src/Parameters/Specifics/Value_molecule.hpp | 33 ++++ src/Parameters/{ => Specifics}/Value_string.cpp | 6 + src/Parameters/{ => Specifics}/Value_string.hpp | 3 + src/Parameters/Value.hpp | 5 +- src/UIElements/Makefile.am | 1 + src/UIElements/Qt4/QtMainWindow.cpp | 1 + src/UIElements/Qt4/Query/FileQtQuery.cpp | 2 +- src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp | 2 +- src/UIElements/Views/Qt4/QtHomologyList.cpp | 44 +++-- src/UIElements/Views/Qt4/QtToolBar.cpp | 11 +- src/UIElements/Views/Qt4/QtToolBar.hpp | 74 +++++++- .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp | 199 ++++++++++++++++++++ 20 files changed, 619 insertions(+), 89 deletions(-) copy src/{Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp => Parameters/Specifics/Value_atom.cpp} (52%) create mode 100644 src/Parameters/Specifics/Value_atom.hpp copy src/{Actions/toPythonString.cpp => Parameters/Specifics/Value_element.cpp} (52%) create mode 100644 src/Parameters/Specifics/Value_element.hpp create mode 100644 src/Parameters/Specifics/Value_molecule.cpp create mode 100644 src/Parameters/Specifics/Value_molecule.hpp rename src/Parameters/{ => Specifics}/Value_string.cpp (92%) rename src/Parameters/{ => Specifics}/Value_string.hpp (83%) create mode 100644 src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.7 deleted. v1.4.7
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

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 "MoleCuilder". The branch, Candidate_v1.4.7 has been deleted was 29b35efc972c36f104ccae2ad8b50ce095b475e8 ----------------------------------------------------------------------- 29b35efc972c36f104ccae2ad8b50ce095b475e8 Set version to 1.4.7. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch ThreadFixes created. v1.4.7-20-g2b11dfb
by git＠ins.uni-bonn.de 15 Sep '14

15 Sep '14

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 "MoleCuilder". The branch, ThreadFixes has been created at 2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b (commit) - Log ----------------------------------------------------------------- commit 2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 21:26:17 2014 +0200 Cleaned up use of mutexes in ActionQueue. - tempqueue now has its own mutex. - more often using lock_guard. - run_thread_isIdle has own mutex. commit 13102c09392ef451c7547ec206917e96beeb1fad Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 19:21:08 2014 +0200 Added extra flag run_thread_running to ActionQueue. - helgrind admonished race conditions when thread is joined. This did not fix them but should be safer as we cannot know whether the other thread has already been started when suddenly shutting down molecuilder due to an exception. commit bc2d4676ddd23758665398fbacb74e40e7fdb45b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 29 11:46:02 2014 +0200 THREADFIX: Fixed ActionQueue with respect to mutex and threads. - run_thread is now last member variable, hence started after all other variables are initialized. - separated accesses to queues and to run_thread_isIdle flag. Also renamed its mutex for easier association with it. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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