Minor bug fix

• Fixes an issue when GROMACS was installed with a buggy version of CMake.
• Update some documentation.

gmxapi 0.0.7.4 for GROMACS 2019

Bug fixes for gmxapi 0.0.7 on GROMACS 2019.

• #232 Invalid attempt to use Context.rank in Context.work setter
• #234 Logic error when checking for operation implementations

gmxapi 0.0.7.3

Minor bug fix that affected some forms of manipulating MD plugins.

gmxapi 0.0.7.2

This is the last planned release of the 0.0.7 gmxapi Python package for GROMACS 2019, unless documentation or bug fixes are necessary.

Warning: This release now requires C++ 14. Previous releases only required C++ 11.

Refer to documentation and to tracked issues for change details.

gmxapi 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

gmxapi 0.0.6

Updated gmx Python package for gmxapi 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.

Also reference DOI 10.1093/bioinformatics/bty484

gmxapi 0.0.5

This release includes some documentation updates and minor improvements over 0.0.4, but primarily serves as a synchronization point for the three repositories: gromacs-gmxapi, gmxapi, and sample_restraint.

gmxapi 0.0.4

Merge pull request #17 from kassonlab/eirrgang-patch-1

Update version info