Change Log

0.0.7

Interface and feature updates

• gmx.context.Context is generic (ParallelArrayContext, DefaultContext deprecated)
• gmx.system.System deprecated (use gmx.workflow.from_tpr())
• Add end_time keyword argument to gmx.workflow.from_tpr()

Deprecation

• steps keyword argument to gmx.workflow.from_tpr() is deprecated in accordance with changes planned for GROMACS 2020.

Internal

• substantial updates for compatibility with GROMACS 2019
• various improvements to CI testing
• Context functionality is now composed according to available resources. (Resource tags, such as ensemble_update will be specified in workspec version 0.2 before the gmxapi 0.1 release.)

Bug fixes

• gmx.get_context() and gmx.run() did not behave as expected for all work types.
• substantial documentation updates

0.0.6

Interface and feature updates

• Updates to gmx.version module
• Automatically set and restore from MD simulation checkpoints in the session working directory.
• Allow control of whether simulation output is appended or truncated (PR #126).
• Allow plugins to issue a stop signal to MD simulations (reference #62 for gromacs-gmxapi and sample_restraint repos).
• Changes to gmx.exceptions
• Allow full CMake-driven install
• Updated example notebooks in sample_restraint repository.

Internal

• Improved CI testing
• #64 Unique work spec identification.

Bug fixes

• #66 Docker does not access current gmxpy version.
• #123 Race condition in session closing.

0.0.5

• allow multiple MD restraints
• documentation updates
• provide Dockerfile for convenience
• continuous integration testing on Travis-CI

0.0.4

Initial beta with support for pluggable pair restraints