Releases: alchemistry/alchemlyb
1.0.0
The 1.0.0 release of alchemlyb comes with a stable API and multiple enhancements for postprocessing and workflows.
Importantly, the 1.x release of alchemlyb only supports pymbar >=3.0.5, <4. We plan to switch to pymbar >= 4 soon (see #205 , #207) and then release a 2.0.0 of alchemlyb. We will not backport fixes from 2.x to 1.x or maintain a 1.x for the long term (unless volunteers from the community offer to take on maintenance).
Supported platforms
We follow NEP29 for supported Python/numpy versions. Currently supported:
- Python 3.8 – 3.10 (continuously tested), 3.11 (manually tested)
- Linux, macOS, Windows
- pymbar >= 3.0.5, < 4
Packages are available from PyPi and conda-forge.
Highlights
- stable API
- complete absolute binding free energy (ABFE) workflow (#114, #231) in the new workflow module (#188)
- more robust AMBER parser (#221, #225, #226, #227, #229, #238)
- new fractional equilibration time convergence analysis (
$R_c$ and$A_c$ from Fan et al 2021) - common
extract(file, temperature)function to read both dHdl and u_nk data in one pass if possible (#222)
For all changes in this release see CHANGES.
Contributors
Contributors
Assets 2
0.7.0
Release with bug fixes and new functionality.
Highlights
- gmx parser now defaults to dropping NaN and corrupted lines (filter=True) #171
- add a base class for workflows (PR #188)
- add filter function to gmx.extract to make it more robust (PR #183): can filter incomplete/corrupted lines (#126, #171) with
filter=True. - Fixed subsampling in
statistical_inefficiency()when lower or step keywords are used (Issue #198, PR #199)
All Changes
See CHANGES for details.
0.6.0
Release with new functionality.
Please note that the GitHub Discussions forum is now enabled where you can ask questions and get involved in the next steps for alchemlyb.
Highlights
- support for NAMD Interleaved Double-Wide Sampling (IDWS) (PR #135)
- various improvements to the robustness of parsing NAMD fepout files (#145)
- forward/backward convergence analysis in the new alchemlyb.convergence module (PR #168)
- automatic MBAR solver (AutoMBAR) that falls back to a potentially more stable solver mode (#170)
- Python 3.10 is fully supported
All changes
See the CHANGES file for details.
0.5.1
0.5.0
This is a major new release of alchemlyb.
Highlights/Important Changes
-
alchemlyb adopts NEP29 to effectively only support the last 2-3 minor Python versions. (#140)
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
-
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).
- postprocessors.units module for unit conversion
- pass_attrs decorator for safely passing unit metadata
- alchemlyb.concat() added to replace pd.concat to ensure correct unit metadata propagation
Functions in the alchemlyb.visualisation module are now able to plot the data in different units.
-
The scipy constant for gas constant R 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. Results in kJ/mol or kcal/mol remain the same if the conversion was performed with the old or new values of R, respectively.
