Gromacswrapper

orbeckst

* added testing for GROMACS 2023.1 (251)
* use black for uniformly formatted code (246)
* minor doc/installation updates
* NOTE: GROMACS 2023 replaced `gmx do_dssp` with `gmx dssp` which is
not directly argument-compatible so GromacsWrapper does NOT alias
it. Therefore, scripts relying on `gromacs.do_dssp` will
break. (249)
* fixed unclosed file in config.py (244)

orbeckst

* fix supported Python metadata in setup.py (238)

orbeckst

* confirmed support for GROMACS 4.6.5, 2018, 2019, 2020, 2021, 2022 on
Python 2.7 and 3.6--3.11 on Linux and macOS
* replaced deprecated logger.warn() with logger.warning() (229)
* replaced deprecated numpy.bool with bool in a test (234)
* fixed use of moved collections.Iterable in test (235)

NOTE: since 0.8.3, the conda package is available from conda-forge
(thanks to njzjz)

orbeckst, simonbray

* conda package (created by simonbray for bioconda) (109)
* fixed stop_logging() fails with NameError (211)

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* fixed: xpm.to_df() used outdated convert_objects()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)