Published August 7, 2025 | Version 4.1.0
Software Open

choderalab/pymbar: 4.1.0 Bugfix Release

Creators

  • 1. University of Colorado Boulder
  • 2. @MolSSI at Virginia Tech
  • 3. Memorial Sloan Kettering Cancer Center
  • 4. @quansight
  • 5. New York University
  • 6. @choderalab & @OpenFreeEnergy
  • 7. @rahko-ai
  • 8. Open Molecular Software Foundation
  • 9. @openforcefield @omsf
  • 10. @NVIDIA @rapidsai
  • 11. Heriot Watt University
  • 12. Datryllic LLC
  • 13. The Open Molecular Software Foundation

Description

This release fixes some typos in documentation and adds some clarity. Some bugs that affected users have been fixed:

  • Index error in subsample_correlated_data https://github.com/choderalab/pymbar/issues/552
  • Verbose=True with MBAR results in an error for alternative input types of u_kn https://github.com/choderalab/pymbar/issues/538
  • Make MBAR bootstrapping deterministic independent of verbose flag https://github.com/choderalab/pymbar/pull/551

Details below :point_down:

What's Changed

  • fix minor typos by @schuhmc in https://github.com/choderalab/pymbar/pull/527
  • Issue gitignore by @jaclark5 in https://github.com/choderalab/pymbar/pull/537
  • Use self.u_kn when verbose=True in MBAR by @jaclark5 in https://github.com/choderalab/pymbar/pull/539
  • Issue docstring harmonic by @jaclark5 in https://github.com/choderalab/pymbar/pull/541
  • Clarify n_bootstraps docstring by @IAlibay in https://github.com/choderalab/pymbar/pull/549
  • Correct Defaults in MBAR Docstring and Fix Typos by @badisa in https://github.com/choderalab/pymbar/pull/550
  • Fix issue 552 by @mikemhenry in https://github.com/choderalab/pymbar/pull/558
  • Fix PyPI package name by @k-ujihara in https://github.com/choderalab/pymbar/pull/559
  • Make MBAR bootstrapping deterministic independent of verbose flag by @badisa in https://github.com/choderalab/pymbar/pull/551
  • Fix version info and modernize some things by @mikemhenry in https://github.com/choderalab/pymbar/pull/562

New Contributors

  • @schuhmc made their first contribution in https://github.com/choderalab/pymbar/pull/527
  • @jaclark5 made their first contribution in https://github.com/choderalab/pymbar/pull/537
  • @IAlibay made their first contribution in https://github.com/choderalab/pymbar/pull/549
  • @k-ujihara made their first contribution in https://github.com/choderalab/pymbar/pull/559

Full Changelog: https://github.com/choderalab/pymbar/compare/4.0.3...4.1.0

Files

choderalab/pymbar-4.1.0.zip

Files (17.4 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/choderalab/pymbar/tree/4.1.0 (URL)

Software

Repository URL
https://github.com/choderalab/pymbar