Releases | Open Source Science

What's Changed

make zenodo archive title identical to JOSS paper title by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/404
[doc] tutorial: use alchemlyb.concat by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/399
2.4.1 by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/405
fix futurewarning for pandas get_groups() by @jaclark5 in https://github.com/alchemistry/alchemlyb/pull/407

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.4.0...2.4.1

Scientific Software - Peer-reviewed - Python
Published by orbeckst over 1 year ago

What's Changed

fixed one remaining wrong date in CHANGES by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/391
Moving average by @jaclark5 in https://github.com/alchemistry/alchemlyb/pull/381
add CITATION.cff file by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/395
Resolve bug in barmodel.deltaf_ creation by @jaclark5 in https://github.com/alchemistry/alchemlyb/pull/397
prepare release 2.4.0 by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/398

New Contributors

@jaclark5 made their first contribution in https://github.com/alchemistry/alchemlyb/pull/381

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.3.2...2.4.0

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 1 year ago

What's Changed

Add a tutorial section by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/379
replace doc footer by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/384
Prepare for 2.3.2 by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/390

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.3.1...2.3.2

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 1 year ago

What's Changed

adopt SPEC 0 instead of NEP 29 by @orbeckst in https://github.com/alchemistry/alchemlyb/pull/370
Support matplotlib 3.9.0 by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/377
Prepare 2.3.1 by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/378

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.3.0...2.3.1

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 1 year ago

What's Changed

capitalize GROMACS in documentation code example by @helmutcarter in https://github.com/alchemistry/alchemlyb/pull/356
clarify docs by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/353
Speed up the MBAR calculation by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/357
Improve the error handling in the backward and forward convergence by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/358

New Contributors

@helmutcarter made their first contribution in https://github.com/alchemistry/alchemlyb/pull/356

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.2.0...2.3.0

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 1 year ago

Changes - Require pandas >= 2.1 (PR #340) - For pandas>=2.1, metadata will be loaded from the parquet file (issue #331, PR #340). - add support for Python 3.12, remove Python 3.8 support (issue #341, PR #304).

Enhancements - Add a TI estimator using gaussian quadrature to calculate the free energy. (issue #302, PR #304) - Warning issued when the series is None for statistical_inefficiency (issue #337, PR #338) - ValueError issued when df and series for statistical_inefficiency doesn't have the same length (issue #337, PR #338)

Fixes - data_fraction column in workflow.convergence won't be affected by the unit conversion (issue #350, PR#319).

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.1.0...2.2.0

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 1 year ago

alchemlyb - 2.1.0

New Minor release.

From this release, loguru is used for logging and pandas parquet file can be used for saving and loading dataframe.

Changes

ValueError raised if concatenated amber output file is passed to amber parser (issue #315, PR #326).
Change the % based string formatting to {} based string formatting (issue #323, PR #324).
Use loguru instead of logging for log (issue #301, PR #303).

Enhancements

"Statistical inefficiency" is logged at debug level for equilibriumdetection and statisticalinefficiency (issue #295, PR#325).
Add a parser to read serialised pandas dataframe (parquet) (issue #316, PR#317).
workflow.ABFE allow parquet as input (issue #316, PR#317).
Allow MBAR estimator to use bootstrap to compute error (issue #320, PR#322).

Fixes

Fix the case where visualisation.plot_convergence would fail when the final error is NaN (issue #318, PR#319).

DeprecationWarning

The default MBAR error estimator in workflow.ABFE.estimate will change from analytic to bootstrap=50 in 2.2.0 (issue #320, PR#322).

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.0.1...2.1.0

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 2 years ago

alchemlyb - 2.0.1

New patch release with bug fix.

What's Changed

Fix the dE method in u_nk2series to use the difference between two lambda columns instead of using the next lambda column or the previous column for the last window (issue #299, PR #300). @xiki-tempula
workaround hanging tests on Mac M1 by using Path.glob instead of glob.glob in ABFE workflow (issue #309, PR #310). @xiki-tempula

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/2.0.0...2.0.1

Scientific Software - Peer-reviewed - Python
Published by xiki-tempula over 2 years ago

alchemlyb - 2.0.0

New major release with backwards-incompatible changes.

The 2.x releases of alchemlyb are based on pymbar release ≥ 4.0.0 (see Discussion #205 ). Compared to the 1.x releases of alchemlyb, which were based on pymbar ≥3.0.5,<4, the API for the estimators.MBAR estimator underwent small changes and alchemlyb's AutoMBAR estimator was removed because the new pymbar MBAR estimator provides its own robust minimizer method selection approach. Code that was written for alchemlyb 1.x will likely run but because pymbar itself went through a major release, we advise caution and careful checking of all results. Compare the output of alchemlyb 1.0.1 (the last release that uses pymbar 3.x) to output from the current alchemlyb 2.0.0.

What's Changed

use pymbar 4 for estimators by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/268
create output directory when it didn't exist for workflow by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/290
raise Exception when no file has been matched in ABFE workflow by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/289

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/1.0.1...2.0.0

Scientific Software - Peer-reviewed - Python
Published by orbeckst about 3 years ago

alchemlyb - 1.0.1

Patch-level release with bug-fixes.

Note that AutoMBAR is being deprecated and scheduled for removal in release 2.0.0 because the MBAR estimator in pymbar 4.0 already provides the equivalent functionality. alchemlyb 2.0.0 will only support pymbar >= 4.0.

(We only fixed the docs and restructured some tests but these changes do not affect user-facing behavior.)

Fixes

#272 : AMBER parser had a "too strict" regex to extract values by @DrDomenicoMarson in https://github.com/alchemistry/alchemlyb/pull/273
#274 : Slicing will no longer drop the NaN rows by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/275
#276 : ABFE workflow crashed with forwrev=0 by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/282

Deprecations

#284 : deprecated AutoMBAR by @xiki-tempula in https://github.com/alchemistry/alchemlyb/pull/285

Full Changelog: https://github.com/alchemistry/alchemlyb/compare/1.0.0...1.0.1

Scientific Software - Peer-reviewed - Python
Published by orbeckst about 3 years ago

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 ( $Rc$ and $Ac$ 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

@xiki-tempula
@DrDomenicoMarson
@orbeckst

Scientific Software - Peer-reviewed - Python
Published by orbeckst about 3 years ago

alchemlyb - 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.

Scientific Software - Peer-reviewed - Python
Published by orbeckst over 3 years ago

alchemlyb - 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.

Scientific Software - Peer-reviewed - Python
Published by orbeckst almost 4 years ago

alchemlyb - 0.5.1

Fixes for bugs and documentation (see CHANGES).

Includes an update to the mission (see Discussion #159) to also include robust and general workflows.