JOSS paper

[orbeckst]

Short software paper for submission to the Journal of Open Source Software.

The paper will be part of the GromacsWrapper repository; this appears to be the common pattern with other JOSS papers.

• submission instructions
• review criteria

Closes Issue #147 (This branch will be merged when the paper is submitted.)

Author contributions

• read #147 for criteria for inclusion
• reply to #147 and state that you want to be an author
• for right now: fork the repo and submit PRs against the paper branch or try to edit the paper.md directly on GitHub.

[orbeckst]

You can start by updating your author meta data in

• paper.md
• codemeta.json

Follow the examples in the file.

[codecov[bot]]

Codecov Report

Merging #158 into master will not change coverage. The diff coverage is n/a.

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##           master     #158   +/-   ##
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  Coverage   62.63%   62.63%           
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  Files          21       21           
  Lines        4135     4135           
  Branches      662      662           
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  Hits         2590     2590           
  Misses       1359     1359           
  Partials      186      186

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Continue to review full report at Codecov.

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[pslacerda]

I'm a bit worried about the acceptance criteria of JOSS. Even if super convenient, this library is largely a python binding to Gromacs command line interface, and they are somewhat strict about bindings. What do you think?

And what about I'm expect to write? Automatic cached documentation generated from the original tools? Was nice to found the performance issue using the profiler, someone with internal knowledge could find intuitively, but for foreigners is easy to find the spot only profiling.

[pslacerda]

I would say it pass the criteria because of lots of working knowledge packed in GromacsWrapper. Just by reading the examples was helpful to improve my Gromacs workflows. For example, I'm doing my first membrane simulation and didn't know that was handy to align the membrane on the XY plane with trj_xyfitted.

[PicoCentauri]

Probably its my fault but I was not able to push my meta data to the PR. Are there any things I have to consider?