Changelog for Humans

This release removes a deprecated numpy function and switches to a supported one. See our release history for more details.

Changelog generated by a robot

• Numpy 2.3 fix (tostring -> tobytes) by @IAlibay in #793
• Changelog for release 0.25.3 by @mikemhenry in #794

Full Changelog: 0.25.2...0.25.3

This release fixes a bug caused by the use of an incorrect API from the warnings module. The issue could trigger errors when retrying simulations that had previously resulted in temporary NaNs.

What's Changed

• Revert to using warnings.warn by @ijpulidos in #790

Full Changelog: 0.25.1...0.25.2

This release fixes a bug where get_entropy() and get_enthalpy() would return an AttributeError when using pymbar4.
See #757 for more details.

This release fixes deprecation warnings for pkg_resources and warnings.warn.
Replaced scipy.integrate.quadrature with scipy.integrate.quad to enable scipy >= 1.15.0 support.
See #788 for more details.

What's Changed

• Pymbar4 entropy enthalpy by @ijpulidos in #785
• Dropping macos-13 (legacy) tests in CI by @ijpulidos in #786
• release 0.25.1 by @mikemhenry in #788

Full Changelog: 0.25.0...0.25.1

What's new?

These release allows online_analysis_interval and checkpoint_interval to be set to different intervals.

Release notes for humans here.

What's Changed

• Remove restriction on online_analysis_interval and checkpoint_interval by @ianmkenney in #779
• Release 0.25.0 by @mikemhenry in #782
• Release 0.25.0 (again) by @mikemhenry in #783

Full Changelog: 0.24.2...0.25.0

This release enables numpy 2 support and makes the FIRE minimization more stable by disabling the barostat during the minimization.

See release notes for humans here.

What's Changed

• Add AWS Tags by @mikemhenry in #766
• chore: migrate to new OMSF start/stop runners by @ethanholz in #775
• Fixes for numpy 2.0 (ruff NPY201) by @IAlibay in #777
• Disable the barostat during FIRE minimization by @hannahbaumann in #773
• release 0.24.2 by @mikemhenry in #778

New Contributors

• @ethanholz made their first contribution in #775
• @hannahbaumann made their first contribution in #773

Full Changelog: 0.24.1...0.24.2

Enhancements

• MultiStateReporter now accepts variable position and velocity checkpointing intervals by @ianmkenney in #767 . Note that when resuming you have to specify again the keyword arguments for the reporter.

New Contributors

• @ianmkenney made their first contribution in #767

Full Changelog: 0.24.0...0.24.1

0.24.0 - pyMBAR Behavior Changes + HIP Platform Added

Bug Fixes

• Update docstring default for alchemical_pme_treatment (Pull Request #644).

Behavior Changes

• Use robust solver for pyMBAR by default.
  pyMBAR 3 & 4 used two different solvers by default.
  Now, the robust solver is used as the default regardless of the pyMBAR version.
  The solver specified in analysis_kwargs (e.g., analysis_kwargs["solver_protocol"] = "robust") is still respected, but if no solver is specified, it defaults to robust.
  This change aims to improve convergence performance (Pull Request #735).

Enhancements

• HIP Platform for OpenMM:
  Added OpenMM's "HIP" platform as a selectable option.
  With OpenMM 8.2, the "HIP" platform is now available for compatible AMD GPUs.
  This enables openmmtools to automatically select the HIP platform if available (Pull Request #753).

• effective_length in MultiStateSamplerAnalyzer:
  Added the effective_length feature (Pull Request #589).

• New alchemy Subpackage:
  Created a subpackage for alchemical computations (Pull Request #721).

Testing

• Framework Overhaul:
  Migrated testing framework to pytest.
  Flaky tests are now automatically re-run (Pull Request #714, Pull Request #746, Pull Request #749, Pull Request #751).

• GPU Testing:
  Testing on GPUs now uses OMSF's gha-runner.

Bugfix

• Fix issue where if None was used for online_analysis_interval an error would be thrown by @mikemhenry in #710

CI

• update self hosted runner to use new setup by @mikemhenry in #670

Full Changelog: 0.23.0...0.23.1

0.23.0 - latest numba support and real time stats enhancements

Please note that there is an API breaking change. To ensure consistency of the data when appending real time stats make sure that you make the online_analysis_interval of your MultiStateSampler object match the checkpoint_interval of your MultiStateReporter. It will error if this is not the case.

Enhancements

• Running with NVIDIA GPUs in Exclusive Process mode now raises a warning (issue #697, PR #699)

Bugfixes

• Fix metadata for netcdf files, specifying openmmtools for the program metadata (issue #694, PR #704).
• Real time statistics YAML file gets appended instead of overwritten when extending or resumimng simulations (issue #691, PR #692).
• Error when resuming simulations with numba 0.57 fixed by avoiding using numpy.MaskedArray when deserializing .nc files (issue #700, PR #701)

Full Changelog: 0.22.1...0.23.0

Bugfixes

• Fix NaN-catching text in MultiStateSampler by @dwhswenson in #684

Full Changelog: 0.22.0...0.22.1