2.4.1

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

2.4.0

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

2.3.2

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

2.3.1

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

2.3.0

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

2.2.0

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

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 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

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: 2.0.0...2.0.1

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 #268
• create output directory when it didn't exist for workflow by @xiki-tempula in #290
• raise Exception when no file has been matched in ABFE workflow by @xiki-tempula in #289

Full Changelog: 1.0.1...2.0.0

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 #273
• #274 : Slicing will no longer drop the NaN rows by @xiki-tempula in #275
• #276 : ABFE workflow crashed with forwrev=0 by @xiki-tempula in #282

Deprecations

• #284 : deprecated AutoMBAR by @xiki-tempula in #285

Full Changelog: 1.0.0...1.0.1