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# -*- tab-width: 2; indent-tabs-mode: nil; coding: utf-8 -*-
====================
alchemlyb CHANGELOG
=====================
The rules for this file:
* entries are sorted newest-first.
* summarize sets of changes - don't reproduce every git log comment here.
* don't ever delete anything.
* keep the format consistent (79 char width, M/D/Y date format) and do not
use tabs but use spaces for formatting
* accompany each entry with github issue/PR number (Issue #xyz)
* release numbers follow "Semantic Versioning" https://semver.org
------------------------------------------------------------------------------
09/17/2021 xiki-tempula, orbeckst
* 0.5.1
Changes (not affecting code)
- update the Mission to also include general and robust workflows (discussion
#159, issue #160, PR #161)
Fixes
- MBAR estimator now correctly passes max_iterations to pymbar.MBAR. (PR #162)
- docs (PR #157)
- visualisation.df_state.plot_dF_state() now correctly raises ValueError instead
of NameError when incorrect orientation keyword argument is supplied
08/01/2021 xiki-tempula, orbeckst
* 0.5.0
Changes
- alchemlyb adopts NEP29
https://numpy.org/neps/nep-0029-deprecation_policy.html
to effectively only support the last 2-3 minor Python versions
- Removed support for Python 2.7 and 3.6 (issue #130, #140):
supported/tested Python versions are 3.7, 3.8, 3.9 on
Linux, macOS, and Windows
- The scipy constant for gas constant is used for parsers instead of the
constants used by the corresponding MD engine (issue #125, PR #129).
This leads to small changes in results from GROMACS simulations in kT
compared to the previous releases, with a relative difference on the order
of 1e-7.
- Added unit-awareness: the base unit remains kT but dataframes need to
carry the unit and temperature in a DataFrame.attrs so that dataframes
can be easily converted to different energy units (issue #125)
- The parser outputs dataframe with metadata (issue #125, PR #129).
- Visualisation module will change the data according to input unit
(issue #125, PR #129).
- Bump the minimum pandas version to 1.2 (issue #130, #140).
Enhancements
- postprocessors.units module for unit conversion (issue #125, PR #129).
- pass_attrs decorator for safely passing variable (issue #125, PR #129).
- alchemlyb.concat added to replace pd.concat (issue #125, PR #129).
Fixes
- `alchemlyb.concat()` should raise ValueError when given empty list, to be
compatible with pandas.concat() (issue #150, PR #152).
- Fix the support for pandas >= 1.3 by skipping 1.3.0 (issue #147, PR #148).
- Fix separate_dhdl not work for multiple columns (issue #149, PR #151).
06/08/2021 orbeckst
* 0.4.2
Fixes
- added back documentation that was lost in 0.4.1 release (#136)
06/01/2021 xiki-tempula, orbeckst
* 0.4.1
Enhancements
Deprecations
- Last release that supports Python 3.5 and 2.7.
Fixes
- The plotting function assumes that the default unit is kcal/mol where it is
kT (issue #124, PR #123).
- invalid escape sequence in plotting annotations (issue #133)
Changes
04/27/2021 wehs7661, dotsdl, xiki-tempula, orbeckst
* 0.4.0
Enhancements
- Allow the dhdl from TI estimator to be separated for multiple lambda
(PR #121).
- Allow the convergence to be plotted. (PR #121)
- Allow automatic sorting and duplication removal during subsampling
(issue #118, PR #119).
- Allow statistical_inefficiency to work on multiindex series. (issue #116,
PR #117)
- Allow the overlap matrix of the MBAR estimator to be plotted. (issue #73,
PR #107)
- Allow the dhdl of the TI estimator to be plotted. (issue #73, PR #110)
- Allow the dF states to be plotted. (issue #73, PR #112)
Deprecations
- Last version that is tested against Python 3.5 and 2.7.
Fixes
- removed redundant statistical inefficiency calculation in
`alchemlyb.preprocessing.subsampling.equilibrium_detection`
Changes
01/16/2020 dotsdl, orbeckst
* 0.3.1
Enhancements
Deprecations
Fixes
- added explicit `return_theta=True` for call to pymbar.MBAR.getFreeEnergyDifferences,
as this was happening prior to changes in `pymbar` without the explicit call
Changes
08/05/2019 dotsdl, orbeckst, shuail, trje3733, brycestx, harlor, vtlim, lee212
* 0.3.0
Enhancements
- Amber TI parser (#10)
- Amber FEP (MBAR) parser (#42)
- Gromacs extended ensemble parser (#14)
- NAMD FEP parser (#7, #75)
- BAR estimator (#40)
- enhanced performance of Gromacs parsers with pandas.read_csv() (#81)
- GOMC TI and FEP parser (#77)
Deprecations
Fixes
- fixed TI estimator (PR #61)
- correctly use pV and U in the Gromacs parser (#59)
Changes
- defaults for statistical_inefficiency() are more conservative (#39)
- API Proposal was upgraded to API Principles (and updated)
(Note: release number 0.2.x was skipped.)
05/27/2017 dotsdl, ianmkenney, orbeckst
* 0.1.0
First release
Features:
- Parsers for GROMACS, including reduced potentials and gradients.
- Subsampler functions for slicing, statitistical inefficiency, equilibration detection.
- Minimally functional estimators for MBAR, TI.
- high test coverage (works with data in alchemistry/alchemtests)