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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
------------------------------------------------------------------------------
12/09/2022 DrDomenicoMarson, xiki-tempula, orbeckst
* 1.0.1
Fixes
- make workflow.ABFE handle 0 as input to forwrev instead of crashing
(issue #276, PR #282).
- Remove most of the iloc in the tests (issue #202, PR #254).
- AMBER parser now raises ValueError when the initial simulation time
is not found (issue #272, PR #273).
- The regex in the AMBER parser now reads also 'field=value' pairs where
there are no spaces around the equal sign (issue #272, PR #273).
- Pre-processing function slicing will not drop NaN rows (issue
#274, PR #275).
Deprecations
- deprecate AutoMBAR for removal in 2.0 because pymbar 4 already contains
equivalent functionality (issue #284, PR #285).
Internal Enhancements (do not affect API)
- Blackfy the codebase (PR #280).
- Refactor the test to make all the parsing done at conftest level
(issue #206, PR #278).
10/31/2022 orbeckst, xiki-tempula, DrDomenicoMarson
* 1.0.0
Changes
- The 1.x release only supports pymbar 3.x; alchemlyb 2.x will only support
pymbar >= 4.0. (#205)
- Default the units in plot_dF_state, plot_convergence and plot_ti_dhdl to
None. Remove the array input for plot_convergence (issue #247, PR #260).
- Now AMBER parser raises an exception when an inconsinstency in the input
file is found, instead of ignoring the file (issues #227 #238, PR #256)
- Now AMBER parser raises an exception when an inconsistency in MBAR data is
found (PR #253)
- Drop support for py3.7 (Issue #179, PR #214)
- forward_backward_convergence will use AutoMBAR as backend when `MBAR` is
selected as the estimator (PR #114).
- AutoMBAR accepts the `method` argument (PR #114).
- Refactor the subsampling module to unify the behaviour of
equilibrium_detection and statistical_inefficiency (PR #218).
- delta_f_, d_delta_f_, states_ are view of the original object in estimator
(issue #246, PR #252).
Enhancements
- Add u_nk2series and dhdl2series to convert u_nk and dHdl to series (PR
#218).
- Add remove_burnin keyword to decorrelate_u_nk and decorrelate_dhdl (PR
#218).
- Add a base class for workflows (PR #188).
- Add the ABFE workflow (PR #114, PR #231).
- Add R_c and A_c for "fractional equilibration time" convergence analysis
(issue #104, PR #239)
- Add the keyword arg final_error to plot_convergence (#249)
- All parsers now have a 'extract(file, T)' method that returns a dict with
both "dHdl" and "u_nk" data (or None). The AMBER parser when using this
function will read the file just once, extracting all data at once. (issue
#222, PR #240)
Fixes
- documented conda installation (available since 0.6.0) (#192)
- AMBER parsers now use 'ntpr' information to read time properly (issue #221,
PR #224)
- AMBER parsers now skip the reading of averages (issue #226, PR #230)
- AMBER parsers now check if the T provided by the user is the same at which
the simulations were run (issue #225, PR #232)
- changed how int/float are read from AMBER files (issue #229, PR #235)
- substitute the any_none() function with a check "if None in" in the AMBER
parser (issue #236, PR #237)
- Fix dhdl2series and u_nk2series would not reattach the unit. (PR #248)
- Removed the 'dhdl' keyword for uncorrelating the u_nk (see
`u_nk2series()`). Use 'dE' as an alternative or use 'all' (instead of the
deprecated 'dhdl_all') (PR #250).
07/22/2022 xiki-tempula, IAlibay, dotsdl, orbeckst, ptmerz
* 0.7.0
Changes
- Deployment to PyPI is now done automatically using github actions
(Issue #193)
- gmx parser now defaults to dropping NaN and corrupted lines (filter=True)
(#171, PR #183)
- remove broken .zip support from util.anyopen() (PR #197)
Enhancements
- Add filter function to gmx.extract to make it more robust (PR #183): can filter
incomplete/corrupted lines (#126, #171) with filter=True.
- Add support to util.anyopen() for taking filelike objects (PR #197)
Fixes
- Fixes setup.py and setup.cfg to prevent installations with Python versions
lower than 3.7 (Issue #193)
- added AutoMBAR to convergence analysis (#189)
- Fixed subsampling in statistical_inefficiency when lower or step keywords
are used (Issue #198, PR #199)
12/28/2021 schlaicha, xiki-tempula, jhenin, ttjoseph, orbeckst
* 0.6.0
Enhancements
- support Python 3.10
- support for Interleaved Double-Wide Sampling (IDWS) in NAMD (PR #135).
Windows may be split across NAMD .fepout files, allowing for interrupted
and restarted simulations, but each window must be complete (issue #145).
Various malformations of input files are detected, where lambdas do not
monotonically increase or decrease, or are inconsistent or missing.
- Convenience function for decorrelating u_nk and dHdl (PR #163).
- Time convergence function forward_backward_convergence
introduced and plot_convergence now takes dataframe from
forward_backward_convergence as input (PR #168).
- Automatic MBAR solver with fall back (issue #170, PR #172)
Fixes
- Subsampling now works with bounds and step (PR #167, issue #166).
- AMBER parser logger now always logs to alchemlyb.parsers.Amber
instead of the root logger (PR #173)
- updated deprecated pandas aggregation, now using groupby(level).agg (#175)
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)