Gromacswrapper

orbeckst, dldotson, kain88-de, ianmkenney

* support Python 3 (44)
* support Gromacs 2018 (and likely also Gromacs 2016) (96)
* moved numkit to own package now at
https://github.com/Becksteinlab/numkit (#111)
* removed gromacs.analysis legacy code, can now be found
in its own repository
https://github.com/Becksteinlab/gromacswrapper.analysis (#82)
* removed vmd sub-package (112), code now at
https://github.com/Becksteinlab/remote-vmd
* removed obsolete staging sub-package (113)
* removed obsolete gromacs.manager module (115)
* removed obsolete fileformats.itp (and fileformats.preprocessor) (139)
* use versioneer for version management (removed gromacs.version)
* add mdrun_args option to setup.energy_minimize to pass options to
the mdrun that carries out the energy minimization
* set ff (OPLS/AA) and water model (TIP4P) as defaults for
setup.topology()
* changed call signature of scaling.partial_tempering() (PR 138)
* development: master branch instead of develop branch (146)

mohebifar, orbeckst, ianmkenney, PicoCentauri, dotsdl

* fixed TOP parser (61)
* fixed isnan test in ITPData._clean_records (99)
* fixed formatting replacement for molecule name in ITP moleculetype section (98)
* fixed TypeError in numkit.integration.simps_error() (115)
* conversion for lists in Gromacs mdp files added (104)

orbeckst, quantifiedcode-bot

* alias tpbconv <-> convert_tpr was not properly set with Gromacs 5
* fixed cbook.grompp_qtot() (89)
* fixed setup.trj_compact_main() (like 89, spurious -doc argument passed)
* additional tests; reactivated tests for top reader but marked many as
expected failure, i.e. the top reader is considered broken (61)
* code clean up (quantified code recommendations)

pslacerda, orbeckst, ianmkenney

* new Gromacs GMXRC parameter in cfg file: if present and set to a
file then GromacsWrapper sources GMXRC and sets the environment
automatically before setting up the Gromacs commands (55)
* doc strings for Gromacs tools are loaded lazily, which speeds up
the initial import of the library to almost instantaneously (PR 76)
* guess which tools to load automatically if no tools option is provided (68)
* new documentation page on how to set up a cfg file

whitead, dotsdl, orbeckst

* fixed: check_mdrun_success() works now for Gromacs 4 and Gromacs 5
(issue 64)
* fixed: MDRunner working for Gromacs 4 and Gromacs 5 (issue 64)
* fixed setup.energy_minimize() not falling back to single precision
mdrun (issue 63)
* fixed: added missing alias "gmx solvate" <--> "genbox" (issue 62)
* added keyword argument use_shell=True to Command() to make Popen use
the shell
* added template for Gromacs 4.6.x gromacswrapper.cfg
* improved testing

quantifiedcode-bot, orbeckst, jandom, whitead

* requires Python 2.7
* new: gromacs pre-processed topology reader
* Added backwards compatibility for scripts written using Gromacs 4.x syntax with Gromacs 5.x.
Tool calls prefixed with 'G_' will still work. (PR 46, Issue 26)
* removed gridmatmd plugin and GridMAT-MD.pl script (41), fixes
installation issues (40)
* Allows custom prefixes like gmx_mpi:mdrun and gmx:trjconv (48)
* Made it so GromacsWrapper can be imported and tools loaded even if they can't
be executed at import time.