GROMACS development

10/17/2019

01:46 PM GROMACS Task #3154 (New): Update use of Python subprocess for >=3.5

We now require Python 3.5, which means we have improved handling of subprocess stdio. Ref subprocess.run().
We can...

10:40 AM GROMACS Task #3153 (New): Let CMake process module directories earlier to support more modern CMake idioms.

@docs@ and @share@ are processed before @src@, @testing@, and @python_packaging@. If the source directories were proc...

10:15 AM GROMACS Feature #3152 (New): Infrastructure and patterns for expressing public interfaces

This issue can serve as the beginning of a roadmap for how GROMACS 2021 will handle API docs, installed headers, and ...

10/16/2019

06:00 PM GROMACS Bug #3111 (Fix uploaded): sample_restraint testing should not download files

05:07 PM GROMACS Revision b34d9608: Minor tidying to mdrun.py

Rearrange and annotate some code in gmxapi.simulation.mdrun prior to
functional additions.
Change-Id: If9efefce8f756...

05:07 PM GROMACS Revision 1f82e445: Minor clean-up to gmxapi package.

* Resolve some linting warnings and potential import ambiguities.
* Apply recommended pybind iteration mechanism for ...

10:28 AM GROMACS Bug #2722: gmxapi may over-manage RPATH

We should be able to resolve this with less effort when we move to the new testing infrastructure, but the appropriat...

09:09 AM GROMACS Revision 383c1e37: Update gmxapi.version module.

* Improve documentation about `has_feature` optional exception behavior.
* Normalize to FeatureNotAvailableError.
* D...

10/15/2019

06:15 PM GROMACS Feature #3149 (New): Python user interface for obtaining simulation artifacts as files.

h2. Scenario
A user wants to run a simulation and acquire the resulting trajectory in a file with a specific name ...

05:16 PM GROMACS Feature #3148 (New): Roadmap for gmxapi filesystem interactions.

Many tasks need to be identified and resolved to allow abstract and optimized gmxapi data flow. To restrict the scope...