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2015-07-25	Teemu Murtola	Remove Options::isSet()	commit \| commitdiff \| tree
2015-07-25	Teemu Murtola	Add basic grouping to Options	commit \| commitdiff \| tree
2015-07-25	Teemu Murtola	Extract IOptionsContainer from Options	commit \| commitdiff \| tree
2015-07-24	Teemu Murtola	Rename trnio routines	commit \| commitdiff \| tree
2015-07-24	Teemu Murtola	Rename trnio.* to trrio.*	commit \| commitdiff \| tree
2015-07-23	Teemu Murtola	Split espresso I/O routines from confio.cpp	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Split gro I/O routines from confio.cpp	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Split g96 I/O routines from confio.cpp	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Move read_tps_conf() to confio.h	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Add basic tests for reading/writing structure files	commit \| commitdiff \| tree
2015-07-20	Teemu Murtola	Merge release-5-0 into release-5-1	commit \| commitdiff \| tree
2015-07-18	Teemu Murtola	Move Options::setDescription() elsewhere	commit \| commitdiff \| tree
2015-07-18	Teemu Murtola	Change naming convention for C++ interfaces	commit \| commitdiff \| tree
2015-07-10	Teemu Murtola	More gmxfio simplification	commit \| commitdiff \| tree
2015-07-09	Teemu Murtola	Fix -deffnm -multi[dir]	commit \| commitdiff \| tree
2015-07-07	Teemu Murtola	Wrap uses of thread_mpi/mutex.h	commit \| commitdiff \| tree
2015-07-05	Teemu Murtola	Improve gmx help -export Sphinx rebuild behavior	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Fix error wrapping in interactive selection input	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Tests for interactive selection input	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Fix copy-paste bug in gmx distance	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Refactor for testing interactive selection input	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Remove gmx::File (except for File::exists())	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Replace direct uses of gmx::File with streams	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Bump various version numbers	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Make some unit tests use mock file output	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Convert gmxfio to C++	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Remove status messages about Sphinx detection	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Clean up gmxfio includes	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Reorder code within gmxfio	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Further gmxfio cleanup related to xdr handling	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Minor include sorting changes	commit \| commitdiff \| tree
2015-07-01	Teemu Murtola	Clean up unused code from gmxfio	commit \| commitdiff \| tree
2015-06-29	Teemu Murtola	Only accept exact matches for selection keywords	commit \| commitdiff \| tree
2015-06-29	Teemu Murtola	Make some unit tests skip file system access	commit \| commitdiff \| tree
2015-06-27	Teemu Murtola	Document tool changes in 5.1	commit \| commitdiff \| tree
2015-06-25	Teemu Murtola	Move documentation on tool changes from wiki	commit \| commitdiff \| tree
2015-06-17	Teemu Murtola	Minor clean up for refdata.*	commit \| commitdiff \| tree
2015-06-17	Teemu Murtola	Improve logic for automatic selection names	commit \| commitdiff \| tree
2015-06-16	Teemu Murtola	Fix broken links from the old flow chart	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Update help output	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Improve uncrustify Jenkins builds	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Initial docs for Jenkins integration	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Initial build system documentation in dev guide	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Improve Jenkins docs build	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Extend source layout description in dev guide	commit \| commitdiff \| tree
2015-06-11	Teemu Murtola	Script for Jenkins documentation build	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Misc. improvements to docs build system	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Add description of relocatable binaries	commit \| commitdiff \| tree
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
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