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2015-06-09	Teemu Murtola	Resolve one TODO for command line help tests	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Improve user guide text for command line interface	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Fix potential FPE in selection tests	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Refactor rst parsing for console output	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Replace gromacs.7 man page with gmx.1	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Document current help formatting	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Basic support for titles within tool help	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Support rst tables in tool help texts	commit \| commitdiff \| tree
2015-05-28	Teemu Murtola	Improve lists in user guide for selections	commit \| commitdiff \| tree
2015-05-28	Teemu Murtola	Additional selection examples	commit \| commitdiff \| tree
2015-05-25	Teemu Murtola	Overview docs for analysis nbsearch	commit \| commitdiff \| tree
2015-05-24	Teemu Murtola	Include selection keyword details in user guide	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Allow any order for sections in 'gmx help -export'	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Base to get all 'gmx help' contents to user guide	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Avoid crash with empty reference for 'same as' selection	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Add subsection depth to HelpWriterContext	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Add note about atom order in selections	commit \| commitdiff \| tree
2015-05-21	Teemu Murtola	Restructure CommandLineModuleManager tests	commit \| commitdiff \| tree
2015-05-20	Teemu Murtola	Fix handling of real-valued 'to' selection ranges	commit \| commitdiff \| tree
2015-05-20	Teemu Murtola	Fix dependencies for regression test custom target	commit \| commitdiff \| tree
2015-05-20	Teemu Murtola	Some tests for 'gmx help -export rst'	commit \| commitdiff \| tree
2015-05-18	Teemu Murtola	Merge "Merge branch origin/release-5-0"	commit \| commitdiff \| tree
2015-05-17	Teemu Murtola	Move a few defines to buildinfo.h	commit \| commitdiff \| tree
2015-05-13	Teemu Murtola	Remove remaining old-html content	commit \| commitdiff \| tree
2015-05-11	Teemu Murtola	Use single variable for expected Doxygen version	commit \| commitdiff \| tree
2015-05-10	Teemu Murtola	Move some testutils and overview docs to dev guide	commit \| commitdiff \| tree
2015-05-10	Teemu Murtola	Print correct order for include order/style issues	commit \| commitdiff \| tree
2015-05-10	Teemu Murtola	Improve build system for Sphinx	commit \| commitdiff \| tree
2015-05-10	Teemu Murtola	Convert developer manual to rst	commit \| commitdiff \| tree
2015-05-05	Teemu Murtola	Avoid rounding errors affecting results in one test	commit \| commitdiff \| tree
2015-04-24	Teemu Murtola	Add section on naming conventions to dev manual	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Replace more [BR] with rst bullet lists	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Replace some [BR] in help texts with rst literals	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Move flow chart from old-html to Sphinx	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Make (most) HTML links to file formats work again	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Convert file format descriptions to rst	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Generate man pages through Sphinx	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Replace tool HTML help with Sphinx-generated docs	commit \| commitdiff \| tree
2015-02-07	Teemu Murtola	Support more complex fixed position selections	commit \| commitdiff \| tree
2015-01-29	Teemu Murtola	Add input file options that accept missing files	commit \| commitdiff \| tree
2015-01-24	Teemu Murtola	Remove old selection parser error handling code	commit \| commitdiff \| tree
2015-01-24	Teemu Murtola	Improve selection error messages (use exceptions)	commit \| commitdiff \| tree
2015-01-23	Teemu Murtola	Ignore test-only dependency cycles	commit \| commitdiff \| tree
2015-01-20	Teemu Murtola	Make data file path search more reusable	commit \| commitdiff \| tree
2015-01-20	Teemu Murtola	Convert forcefield search to C++	commit \| commitdiff \| tree
2015-01-19	Teemu Murtola	Remove AnalysisNeighborhood::setUseBoundingBox()	commit \| commitdiff \| tree
2015-01-17	Teemu Murtola	Merge "Merge branch release-5-0"	commit \| commitdiff \| tree
2015-01-08	Teemu Murtola	Refactor logic for finding share/top/ files	commit \| commitdiff \| tree
2015-01-08	Teemu Murtola	Closed some .xvg files that were being left open	commit \| commitdiff \| tree
2015-01-07	Teemu Murtola	Custom program context for unit tests	commit \| commitdiff \| tree
2015-01-07	Teemu Murtola	Split unit test init from testoptions.cpp	commit \| commitdiff \| tree
2015-01-06	Teemu Murtola	Use analysis nbsearch for surface area calculation	commit \| commitdiff \| tree
2015-01-06	Teemu Murtola	Use xvgrclose() for files opened with xvgropen()	commit \| commitdiff \| tree
2015-01-05	Teemu Murtola	Support subset of rvec array as input for analysis...	commit \| commitdiff \| tree
2015-01-05	Teemu Murtola	Minimal C++ replacement for rvec	commit \| commitdiff \| tree
2015-01-05	Teemu Murtola	Clarify GMX_MPI management	commit \| commitdiff \| tree
2015-01-03	Teemu Murtola	Minor selection clarifications	commit \| commitdiff \| tree
2015-01-03	Teemu Murtola	Fix crash with 'z of ...' within an expression	commit \| commitdiff \| tree
2015-01-02	Teemu Murtola	Update copyright year in copyrite.cpp	commit \| commitdiff \| tree
2014-12-28	Teemu Murtola	Convert gmx-insert-molecules into proper C++ module	commit \| commitdiff \| tree
2014-12-28	Teemu Murtola	Add helper for generic C++ command-line modules	commit \| commitdiff \| tree
2014-12-18	Teemu Murtola	Rework gmx-solvate to use analysis nbsearch	commit \| commitdiff \| tree
2014-12-17	Teemu Murtola	Make 'gmx sasa' calculation thread-safe	commit \| commitdiff \| tree
2014-12-17	Teemu Murtola	Remove some backwards-compatibility glue for Jenkins	commit \| commitdiff \| tree
2014-12-16	Teemu Murtola	Make 'gmx sasa' volume computation translation-invariant	commit \| commitdiff \| tree
2014-12-15	Teemu Murtola	Use new XML format with cppcheck	commit \| commitdiff \| tree
2014-12-14	Teemu Murtola	C++ interface for surface area calculation	commit \| commitdiff \| tree
2014-12-11	Teemu Murtola	Convert gmx rdf to the C++ framework	commit \| commitdiff \| tree
2014-12-10	Teemu Murtola	Fix misc. analysis neighborhood search issues	commit \| commitdiff \| tree
2014-12-09	Teemu Murtola	Track locations for selection parsing products	commit \| commitdiff \| tree
2014-12-08	Teemu Murtola	Rectangular grid for analysis nbsearch	commit \| commitdiff \| tree
2014-12-06	Teemu Murtola	Simplify analysisdata parallelism model	commit \| commitdiff \| tree
2014-12-05	Teemu Murtola	Improve selection parsing error reporting	commit \| commitdiff \| tree
2014-12-05	Teemu Murtola	Non-periodic nbsearch with grid based on bounding box	commit \| commitdiff \| tree
2014-12-04	Teemu Murtola	Move/add uncrustify documentation to dev manual	commit \| commitdiff \| tree
2014-12-02	Teemu Murtola	Add 'gmx pairdist' tool as partial g_mindist replacement	commit \| commitdiff \| tree
2014-12-02	Teemu Murtola	Analysis grid nbsearch for more cases	commit \| commitdiff \| tree
2014-11-29	Teemu Murtola	Basic support for 'z of ...' selections	commit \| commitdiff \| tree
2014-11-28	Teemu Murtola	Clarify memory management for selection values	commit \| commitdiff \| tree
2014-11-28	Teemu Murtola	Helper function for grouping selection positions	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	Clean up gmx solvate	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	Port gmx-solvate tests to use CommandLineTestBase	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	More control over file backups	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	Further insert-molecules cleanup	commit \| commitdiff \| tree
2014-11-26	Teemu Murtola	Convert surface area calculation to C++	commit \| commitdiff \| tree
2014-11-26	Teemu Murtola	Add some unit tests for surface area calculation	commit \| commitdiff \| tree
2014-11-23	Teemu Murtola	Rename doc-* targets to be less generic	commit \| commitdiff \| tree
2014-11-21	Teemu Murtola	Describe doc-check in developer manual	commit \| commitdiff \| tree
2014-11-21	Teemu Murtola	Skeleton for a developer manual	commit \| commitdiff \| tree
2014-11-14	Teemu Murtola	Refactor position-evaluated selection keyword handling	commit \| commitdiff \| tree
2014-10-30	Teemu Murtola	Add more selection unit tests	commit \| commitdiff \| tree
2014-10-30	Teemu Murtola	Fix more memory leaks in default group creation	commit \| commitdiff \| tree
2014-10-30	Teemu Murtola	Fix memory leak in default index group creation	commit \| commitdiff \| tree
2014-10-29	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2014-10-29	Teemu Murtola	Improve analysis nbsearch grid mapping	commit \| commitdiff \| tree
2014-10-28	Teemu Murtola	Avoid common.h inclusion in CUDA code	commit \| commitdiff \| tree
2014-10-23	Teemu Murtola	Move truncate() wrapper to futil.h	commit \| commitdiff \| tree
2014-10-23	Teemu Murtola	Encapsulate use of nice()	commit \| commitdiff \| tree
2014-10-22	Teemu Murtola	Collect more platform-specific code to sysinfo.h	commit \| commitdiff \| tree
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