New minor release of alchemlyb with fixes and enhancements.

Supports Python 3.11 - 3.14.

See CHANGES for details.

What's Changed

• update action/checkout by @orbeckst in #417
• Parallel read and preprocess the data by @xiki-tempula in #371
• correct error in tutorial for plot_convergence() by @spackman in #422
• Line too long by @evidencebp in #424
• Add entropy and enthalpy by @jaclark5 in #406
• add badge and how to cite by @xiki-tempula in #426
• Fix GMX test by @xiki-tempula in #430
• Fix test by @xiki-tempula in #431
• Use bar_intervall instead of ntpr for parsing AMBER MBAR timestamps by @yuxuanzhuang in #429
• Using ruff to do format and lint check by @xiki-tempula in #432
• Use mypy to do type check by @xiki-tempula in #433
• update type hinting by @orbeckst in #441
• Add Python 3.14 support and update CI/CD workflows by @orbeckst in #440
• prepare for release 2.5.0 by @orbeckst in #443
• clean ups for 2.5.0 release by @orbeckst in #444

New Contributors

• @spackman made their first contribution in #422
• @evidencebp made their first contribution in #424
• @yuxuanzhuang made their first contribution in #429

Full Changelog: 2.4.1...2.5.0

New minor release of alchemlyb with fixes and enhancements. (This is release candidate 1 — functionality will likely be the same as in the final 2.5.0 release but testing, deployment, and documentation may change.)

Supports Python 3.11 - 3.14.

See CHANGES for details.

What's Changed

• update action/checkout by @orbeckst in #417
• Parallel read and preprocess the data by @xiki-tempula in #371
• correct error in tutorial for plot_convergence() by @spackman in #422
• Line too long by @evidencebp in #424
• Add entropy and enthalpy by @jaclark5 in #406
• add badge and how to cite by @xiki-tempula in #426
• Fix GMX test by @xiki-tempula in #430
• Fix test by @xiki-tempula in #431
• Use bar_intervall instead of ntpr for parsing AMBER MBAR timestamps by @yuxuanzhuang in #429
• Using ruff to do format and lint check by @xiki-tempula in #432
• Use mypy to do type check by @xiki-tempula in #433
• update type hinting by @orbeckst in #441
• Add Python 3.14 support and update CI/CD workflows by @orbeckst in #440
• prepare for release 2.5.0 by @orbeckst in #443

New Contributors

• @spackman made their first contribution in #422
• @evidencebp made their first contribution in #424
• @yuxuanzhuang made their first contribution in #429

Full Changelog: 2.4.1...2.5.0rc1

Patch release with minor fixes.

What's Changed

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

Full Changelog: 2.4.0...2.4.1

What's Changed

• fixed one remaining wrong date in CHANGES by @orbeckst in #391
• Moving average by @jaclark5 in #381
• add CITATION.cff file by @orbeckst in #395
• Resolve bug in bar_model.delta_f_ creation by @jaclark5 in #397
• prepare release 2.4.0 by @orbeckst in #398

New Contributors

• @jaclark5 made their first contribution in #381

Full Changelog: 2.3.2...2.4.0

What's Changed

• Add a tutorial section by @xiki-tempula in #379
• replace doc footer by @orbeckst in #384
• Prepare for 2.3.2 by @xiki-tempula in #390

Full Changelog: 2.3.1...2.3.2

What's Changed

• adopt SPEC 0 instead of NEP 29 by @orbeckst in #370
• Support matplotlib 3.9.0 by @xiki-tempula in #377
• Prepare 2.3.1 by @xiki-tempula in #378

Full Changelog: 2.3.0...2.3.1

What's Changed

• capitalize GROMACS in documentation code example by @helmutcarter in #356
• clarify docs by @xiki-tempula in #353
• Speed up the MBAR calculation by @xiki-tempula in #357
• Improve the error handling in the backward and forward convergence by @xiki-tempula in #358

New Contributors

• @helmutcarter made their first contribution in #356

Full Changelog: 2.2.0...2.3.0

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: 2.1.0...2.2.0

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 equilibrium_detection
  and statistical_inefficiency (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: 2.0.1...2.1.0

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: 2.0.0...2.0.1