Release History

Releases follow the major.minor.micro scheme recommended by PEP440, where

  • major increments denote a change that may break API compatibility with previous major releases

  • minor increments add features but do not break API compatibility

  • micro increments represent bugfix releases or improvements in documentation

0.0.9 - Multi-state Reweighting Fix

This release implements a fix for calculating the gradients of properties being estimated by reweighting data cached from multiple independant simulations.

Bugfixes

  • PR #143: Fix for multi-state gradient calculations.

0.0.8 - ThermoML Improvements

This release is centered around cleaning up the ThermoML data set utilities. The main change is that ThermoML archive files can now be loaded even if they don’t contain measurement uncertainties.

New Features

  • PR #142: ThermoML archives without uncertainties can now be loaded.

Breaking Changes

  • PR #142: All ThermoMLXXX classes other than ThermoMLDataSet are now private.

0.0.7 - Bug Quick Fixes

This release aims to fix a number of minor bugs.

Bugfixes

  • PR #136: Fix for comparing thermodynamic states with unset pressures.

  • PR #138: Fix for a typo in the maximum number of minimization iterations.

0.0.6 - Solvation Free Energies

This release centers around two key changes -

  1. a general refactoring of the protocol classes to be much cleaner and extensible through the removal of the old stub functions and the addition of cleaner descriptors.

  2. the addition of workflows to estimate solvation free energies via the new SolvationYankProtocol and SolvationFreeEnergy classes.

The implemented free energy workflow is still rather basic, and does not yet support calculating parameter gradients or estimation from cached simulation data through reweighting.

A new table has been added to the documentation to make clear which built-in properties support which features.

New Features

  • PR #110: Cleanup and refactor of protocol classes.

  • PR #125: Support for PBS based HPC clusters.

  • PR #127: Adds a basic workflow for estimating solvation free energies with YANK.

  • PR #130: Adds a cleaner mechanism for restarting simulations from checkpoints.

  • PR #134: Update to a more stable dask version.

Bugfixes

  • PR #128: Removed the defunct dask backend processes kwarg.

  • PR #133: Fix for tests failing on MacOS due to travis issues.

Breaking Changes

  • PR #130: The RunOpenMMSimulation.steps input has now been split into the steps_per_iteration and total_number_of_iterations inputs.

Migration Guide

This release contained several public API breaking changes. For the most part, these can be remedied by the follow steps:

  • Replace all instances of run_openmm_simulation_protocol.steps to run_openmm_simulation_protocol.steps_per_iteration

0.0.5 - Fix For Merging of Estimation Requests

This release implements a fix for a major bug which caused incorrect results to be returned when submitting multiple estimation requests at the same time - namely, the returned results became jumbled between the different requests. As an example, if a request was made to estimate a data set using the smirnoff99frosst force field, and then straight after with the gaff 1.81 force field, the results of the smirnoff99frosst request may contain some properties estimated with gaff 1.81 and vice versa.

This issue does not affect cases where only a single request was made and completed at a time (i.e the results of the previous request completed before the next estimation request was made).

Bugfixes

  • PR #119: Fixes gather task merging.

  • PR #121: Update to distributed 2.5.1.

0.0.4 - Initial Support for Non-SMIRNOFF FFs

This release adds initial support for estimating property data sets using force fields not based on the SMIRNOFF specification. In particular, initial AMBER force field support has been added, along with a protocol which applies said force fields using tleap.

New Features

  • PR #96: Adds a mechanism for specifying force fields not in the SMIRNOFF spec.

  • PR #99: Adds support for applying AMBER force field parameters through tleap

  • PR #111: Protocols now stream trajectories from disk, rather than pre-load the whole thing.

  • PR #112: Specific types of protocols can now be easily be replaced using WorkflowOptions.

  • PR #117: Adds support for converting PhysicalPropertyDataSet objects to pandas.DataFrame.

Bugfixes

  • PR #115: Fixes caching data for substances whose smiles contain forward slashes.

  • PR #116: Fixes inconsistent mole fraction rounding.

Breaking Changes

  • PR #96: The PropertyEstimatorClient.request_estimate(force_field=... argument has been renamed to force_field_source.

Migration Guide

This release contained several public API breaking changes. For the most part, these can be remedied by the follow steps:

  • Change all instances of PropertyEstimatorClient.request_estimate(force_field=...) to PropertyEstimatorClient.request_estimate(force_field_source=...)

0.0.3 - ExcessMolarVolume and Typing Improvements

This release implements a number of bug fixes and adds two key new features, namely built in support for estimating excess molar volume measurements, and improved type checking for protocol inputs and outputs.

New Features

  • PR #98: Substance objects may now have components with multiple amount types.

  • PR #101: Added support for estimating ExcessMolarVolume measurements from simulations.

  • PR #104: typing.Union is now a valid type arguemt to protocol_output and protocol_input.

Bugfixes

  • PR #94: Fixes exception when testing equality of ProtocolPath objects.

  • PR #100: Fixes precision issues when ensuring mole fractions are <= 1.0.

  • PR #102: Fixes replicated input for children of replicated protocols.

  • PR #105: Fixes excess properties weighting by the wrong mole fractions.

  • PR #107: Fixes excess properties being converged to the wrong uncertainty.

  • PR #108: Fixes calculating MBAR gradients of reweighted properties.

Breaking Changes

  • PR #98: Substance.get_amount renamed to Substance.get_amounts and now returns an immutable frozenset of Amount objects, rather than a single Amount.

  • PR #104: The DivideGradientByScalar, MultiplyGradientByScalar, AddGradients, SubtractGradients and WeightGradientByMoleFraction protocols have been removed. The WeightQuantityByMoleFraction protocol has been renamed to WeightByMoleFraction.

Migration Guide

This release contained several public API breaking changes. For the most part, these can be remedied by the follow steps:

  • Change all instances of Substance.get_amount to Substance.get_amounts and handle the newly returned frozenset of amounts, rather than the previously returned single amount.

  • Replace the now removed protocols as follows:

    • DivideGradientByScalar -> DivideValue

    • MultiplyGradientByScalar -> MultiplyValue

    • AddGradients -> AddValues

    • SubtractGradients -> SubtractValues

    • WeightGradientByMoleFraction -> WeightByMoleFraction

    • WeightQuantityByMoleFraction -> WeightByMoleFraction

0.0.2 - Replicator Quick Fixes

A minor release to fix a number of minor bugs related to replicating protocols.

Bugfixes

  • PR #90: Fixes merging gradient protocols with the same id.

  • PR #92: Fixes replicating protocols for more than 10 template values.

  • PR #93: Fixes ConditionalGroup objects losing their conditions input.

0.0.1 - Initial Release

The initial pre-alpha release of the framework.