forked from Becksteinlab/GromacsWrapper
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathCHANGES
261 lines (211 loc) · 9.91 KB
/
CHANGES
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
==============================
CHANGELOG for GromacsWrapper
==============================
2024-09-18 0.9.1
orbeckst, hsk17
* templates in `config.templates` are now stored as
`importlib.resources.abc.Traversable` (PosixPath-like) objects instead of
strings of paths to files in the file system because we switched from
pkg_resources to importlib.resources for managing access to included files
(#282)
* fixed reporting of failures of GromacsCommand and DeprecationWarnings for use
of \s in regular expression strings (#285)
* fixed use of outdated numpy.NAN | INF by using nan | inf (#290)
* added automatic deployment workflow (using action MDAnalysis/pypi-deployment)
(#295)
2024-06-15 0.9.0
orbeckst, jandom, njzjz
* officially support Python 3.12 (PR #271, issue #263)
* supports GROMACS 2024.2 (PR #280)
* removed support for legacy Python (<= 3.8) (#259)
* fixed GROMACS TOP reader not reading angle parameters from topology
file (#261)
* fixed Python 3.12: No module named ('pkg_resources' #263)
* fixed AttributeDict does not support hasattr (#214)
* fixed handle KeyboardInterrupts when using MDRunner.run() (#252)
* internally switched to pyproject.toml (#278)
* Pending Deprecation for the gw-*.py scripts:
The gw-*.py scripts are NOT anymore installed (it's technically
messy with the new system #278 and requires code refactoring). They
will likely be DEPRECATED. See issue #279 for more details and voice
your opinion if you really need these scripts.
2023-09-16 0.8.5
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)
2023-03-13 0.8.4
orbeckst
* fix supported Python metadata in setup.py (#238)
2023-03-09 0.8.3
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)
2021-09-09 0.8.2
orbeckst, simonbray
* conda package (created by @simonbray for bioconda) (#109)
* fixed stop_logging() fails with NameError (#211)
2021-07-23 0.8.1
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)
2019-04-30 0.8.0
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)
2018-08-08 0.7.0
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)
2017-03-23 0.6.2
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)
2016-09-16 0.6.1
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)
2016-09-09 0.6.0
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
2016-06-29 0.5.1
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
2016-05-23 0.5.0
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.
2015-12-16 0.4.0
orbeckst, richardjgowers
* primitive support for Gromacs 5.x
* fixed: gromacs.fileformats was not imported properly (PR #21)
* docs at http://gromacswrapper.readthedocs.org
2015-05-22 0.3.3
orbeckst, jandom
* improvements to the xpm reader
* improvements to stripwater plugin and transformer
* additional logging of filenames in setup._MD()
* new repository URL: https://github.com/Becksteinlab/GromacsWrapper
2013-08-07 0.3.2
orbeckst, andy.somogyi
* fixed setup.make_main_index() by using a workaround for a bug in make_ndx
when multiple groups have the same name (use the first one)
* improvements in cbook.Transformer and the StripWater plugin (can
write output to specified directory)
* gw-fit_strip_trajectories.py: can use a custom group for centering
(necessary when dealing with multimeric proteins that might get
split across the periodic boundaries)
2012-12-10 0.3.1
orbeckst, jandom
* added IndexBuilder.write() method to safely write named index groups
* new HBonds hydrogen bonding analysis plugin (uses g_hbond and can
return individual hbond existence probabilities)
* XVG has initial support to plot periodic data such as dihedral angles
* ITP reader:
- ITP.contains_preprocessor_constructs() to check if the
itp file uses some of the recognized preprocessing directives
- new set_data() method to completely rebuild a topology
* set environment variable GROMACSWRAPPER_SUPPRESS_SETUP_CHECK to true
in order to avoid be notified of missing config files
* example scripts are installed (all example script names start
with gw-*)
- gw-fit_strip_trajectories.py: remove water and fit to protein
- gw-join_parts.py: concatenate xtc, trr, edr, log for simulations
done in parts (and with -noappend)
- gw-merge_topologies.py: join multiple building block topologies
* updated MDP templates
- increase Parrinello-Rahman time constant to 1.0 ps
- use refcoord_scaling = "com" for position restraints
- use recommended CHARMM NB values
* fixed: cbook.grompp_qtot() would miss non-zero charge
* fixed: Manager config parser ignored floats
* gromacs.setup.solvate()
- default ion names are now NA and CL
- adapted for Gromacs 4.6
- bt takes precedence over boxtype
2012-04-24 0.3.0
orbeckst
* improved file format handling (ITP (incomplete, but uses a
preprocessor), XPM, XVG (can do fairly fancy coarse-grained
plotting and error analysis))
* output can be captured to a capture file (uses the new
gromacs.environment framework)
* fixes for cbook.Transformer
* removed deprecated edPDB (use MDAnalysis instead)
* example script fit_strip_trajectory.py
* scipy is now a package dependency (use in numkit and then XVG)
Earlier releases did not have an explicit change log. See the commit
history at https://github.com/orbeckst/GromacsWrapper for details.