0.17.0 - Removed Py2 support, faster exact PME treatment

New features

• Add GlobalParameterFunction that allows to enslave a GlobalParameter to an arbitrary function of controlling variables (#380).
• Allow ignoring velocities when building the dict representation of a SamplerState. This can be useful for example to save bandwidth when sending a SamplerState over the network and velocities are not required (#386).
• Add DoubleWellDimer_WCAFluid and DoubleWellChain_WCAFluid test systems (#389).

Enhancements

• New implementation of the exact PME handling that uses the parameter offset feature in OpenMM 7.3. This comes with a
  considerable speed improvement over the previous implementation (#380).
• Exact PME is now the default for the alchemical_pme_treatment parameter in the constructor of
  AbsoluteAchemicalFactory (#386).
• It is now possible to have multiple composable states exposing the same attributes/getter/setter in a
  CompoundThermodynamicState (#380).

Bug fixes

• Fixed a bug involving the NoseHooverChainVelocityVerletIntegrator with System with constraints. The constraints were not taken into account when calculating the number of degrees of freedom resulting in the temperature not converging to the target value. (#384)
• Fixed a bug affecting reduced_potential_at_states when computing the reduced potential of systems in different AlchemicalStates when the same alchemical parameter appeared in force objects split into different force groups. (#385)

Deprecated and API breaks

• Python 2 and 3.5 is not supported anymore.
• The update_alchemical_charges attribute of AlchemicalState, which was deprecated in 0.16.0, has now been removed since it doesn't make sense with the new parameter offset implementation.
• The methods AlchemicalState.get_alchemical_variable and AlchemicalState.set_alchemical_variable have been deprecated. Use AlchemicalState.get_alchemical_function and AlchemicalState.set_alchemical_function instead.

0.16.0 - Py2 deprecated, GlobalParameterState class, SamplerState reads CVs

New features

• Add ability for SamplerState to read new OpenMM CustomCVForce variables from the Context object (#362).
• Added the new class states.GlobalParameterState designed to simplify the implementation of composable states that control global variables (#363).
• Allow restraint force classes to be controlled by a parameter other than lambda_restraints. This will enable multi-restraints simulations (#363).

Enhancements

• Global variables of integrators are now automatically copied over the integrator returned by ContextCache.get_context. It is possible to specify exception through ContextCache.INCOMPATIBLE_INTEGRATOR_ATTRIBUTES (#364).

Others

• Integrator MCMCMoves now attempt to recover from NaN automatically by default (with n_restart_attempts set to 4) (#364).

Deprecated

• Python2 is officially deprecated. Support will be dropped in future versions.
• Deprecated the signature of IComposableState._on_setattr to fix a bug where the objects were temporarily left in an inconsistent state when an exception was raised and caught.
• Deprecated update_alchemical_charges in AlchemicalState in anticipation of the new implementation of the exact PME that will be based on the NonbondedForce offsets rather than updateParametersInContext().

0.15.0 - Restraint forces

• Add radially-symmetric restraint custom forces (#336).
• Copy Python attributes of integrators on deepcopy() (#336).
• Optimization of states.CompoundThermodynamicState deserialization (#338).
• Bugfixes (#332, #343).

0.14.0 - Exact treatment of alchemical PME electrostatics, water cluster test system, optimizations

New features

• Add a WaterCluster testsystem (#322)
• Add exact treatment of PME electrostatics in alchemy.AbsoluteAlchemicalFactory. (#320)
• Add method in ThermodynamicState for the efficient computation of the reduced potential at a list of states. (#320)

Enhancements

• When a SamplerState is applied to many Contexts, the units are stripped only once for optimization. (#320)

Bug fixes

• Copy thermodynamic state on compound state initialization. (#320)

0.13.4 - Barostat/External Force Bugfix, Restart Robustness

Bug fixes

• Fixed implementation bug where CustomExternalForce restraining atoms to absolute coordinates caused an issue when a Barostat was used (#310)

Enhancements

• MCMC Integrators now attempt to re-initialize the Context object on the last restart attempt when NaN's are encountered. This has internally been shown to correct some instances where normally resetting positions does not work around the NaN's. This is a slow step relative to just resetting positions, but better than simulation crashing.

0.13.3 - Critical Bugfix to SamplerState Context Manipulation

Critical Fixes

• SamplerState.apply_to_context() applies box vectors before positions are set to prevent a bug on non-Reference OpenMM Platforms which can re-order system atoms and sample the wrong distribution. (#305)

Additional Fixes

• LibYAML is now optional (#304)
• Fix AppVeyor testing against Python 3.4 (now Python 3.5/3.6 and NumPy 1.12) (#307)
• Release History now included in online Docs

0.13.2 - SamplerState Slicing and BitWise And/Or Ops

In this Release:

Added support for SamplerState slicing (#298)
Added bit operators and and or to math_eval (#301)

0.13.1 - Bugfix release

In this release:

• Fix pickling of CompoundThermodynamicState (#284).
• Add missing term to OBC2 GB alchemical Force (#288).
• Generalize forcefactories.restrain_atoms() to non-protein receptors (#290).
• Standardize integrator global variables in ContextCache (#291).

OpenMMTools 0.13.0

This release includes the following features:

• Storage Interface module with automatic disk IO handling
• Option for shifted or switched Reaction Field
• LangevinSplittingDynamic MCMC move with specifiable sub step ordering
• Nose-Hoover Chain Thermostat

Bugs fixed in this release

• Many doc string cleanups
• Tests are based on released versions of OpenMM
• Tests also compare against development OpenMM, but do not fail because of it
• Fixed bug in Harmonic Oscillator tests' error calculation
• Default collision rate in Langevin Integrators now matches docs

0.12.1 - Add virtual sites support in alchemy

In this release:

• Fixed AbsoluteAlchemicalFactory treatment of virtual sites that were previously ignored (#259).
• Add possibility to add ions to the WaterBox test system (#259).