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Feature #3038

Improvements to MD plugin development environment

Added by Eric Irrgang 5 months ago. Updated 5 months ago.

Status:
New
Priority:
Normal
Assignee:
Category:
gmxapi
Target version:
Difficulty:
uncategorized
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Description

This issue is a parent for several improvements to the MD plugin development environment laid out in sample_restraint

https://github.com/kassonlab/sample_restraint is a project that can be forked as the starting point for developing GROMACS 2019 compatible MD plugins for use with gmxapi 0.0.7. For GROMACS 2020 and beyond, the primary source code will be managed under the GROMACS repository. Several improvements are necessary for ongoing GROMACS compatibility and to improve the experience of plugin developers.

  • Create a new skeleton repository that researchers can clone to get the python_packaging/sample_restraint subtree, plus additional project helpers.
  • Improve documentation and set-up of the new project, such as with CookieCutter wrapping.
  • Add more call signatures and use cases for restraint calculation.
  • Update various internals to use modern GROMACS facilities and features.
  • Extract boiler plate to template headers.
  • Modernize expression of inputs, outputs, and factory functions, as enabled in core GROMACS.
  • Prepare template headers to be moved to the GROMACS installed headers (to be moved in GROMACS 2021)
  • Improve documentation and documentation integration with GROMACS manuals.

Related issues

Related to GROMACS - Feature #2896: Python packagingIn Progress
Related to GROMACS - Task #3027: Move sample_restraint development from GitHub to GerritClosed
Related to GROMACS - Task #3040: Refactor Restraint moduleNew

Associated revisions

Revision 75dd2560 (diff)
Added by Eric Irrgang 3 months ago

More templating in sample_restraint.

Start moving towards a template header library to replace the boiler
plate in the sample restraint code. Separate out the most important bits
of a Potential implementation. Use templates to wrap the Restraint
aspect and input/output resources.

Refs #3038

Change-Id: Ice946eb0e6722eafbe75aeae6a45fe872ea602eb

History

#1 Updated by Eric Irrgang 5 months ago

  • Description updated (diff)

#2 Updated by Eric Irrgang 5 months ago

#3 Updated by Eric Irrgang 5 months ago

  • Related to Task #3027: Move sample_restraint development from GitHub to Gerrit added

#4 Updated by Eric Irrgang 5 months ago

  • Description updated (diff)

#5 Updated by Eric Irrgang 5 months ago

  • Related to Task #3040: Refactor Restraint module added

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