Gromacswrapper

orbeckst, PolyachenkoYA, whitead

* confirmed support for GROMACS 4.6.5, 2018, 2019, 2020, 2021 on Python 2.7 and
3.6--3.9 on Linux and macOS (200, 202, 203)
* fixed: core._run_command capture_output_file argument fixed to us python-3.0
file open (181)
* fixed: xvg._decimate used python-2.0-specific func_name() (issue 183)
* fixed: make parsing gmx output more robust to avoid failure on
'import gromacs' (PR 186)
* fixed: xpm.to_df() used outdated convert_objects()
* fixed: gw-forcefield.py use print() function for Py 2/3 compatibility
* fixed: xvg.plot() and xvg.plot_coarsened() failed with Py 3 matplotlib
due to incompatible colors (issue 194)

richardjgowers, theavey, andrejberg, orbeckst

* allow ignoring of gmx executable suffix (such as '_mpi' or '_d' by adding an
option to the configuration file (Issue 124)
* allow reading of compressed XPM files (PR 169)
* fixed MDP round trip writing, string fields no longer mangled
(Issue 149)
* fixed NDX writing (152)
* fixed Python 3 compatibility of XPM reader (PR 169)
* fixed bug in calling logger in fileformats.top (issue 173)
* add gromacs.release() to get release of loaded Gromacs (issue 161)
* tested with Gromacs 2019.1, 2018.4, 4.6.5 (172)

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