Joss-reviews: [REVIEW]: MSMExplorer: Data Visualizations for Biomolecular Dynamics

[whedon]

Submitting author: @cxhernandez (Carlos Xavier Hernández)
Repository: https://github.com/msmexplorer/msmexplorer
Version: v1.0.0
Editor: @arokem
Reviewer: @anotherjoshsmith
Archive: 10.5281/zenodo.439774

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/f9485c45a7bfc5cfce6edd8919a07739/status.svg)](http://joss.theoj.org/papers/f9485c45a7bfc5cfce6edd8919a07739)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v1.0.0)?
• [x] Authorship: Has the submitting author (@cxhernandez) made major contributions to the software?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: Have any performance claims of the software been confirmed?

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g. API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @anotherjoshsmith it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

[arokem]

@arfon : why does this say "Does the release version given match the GitHub release (v1.0.0)?"?

The current release version on Github is 0.3. Where does the 1.0.0 come from?

[cxhernandez]

@arokem: That's my fault. My intention was to hold off on making a v1.0.0 release until the review is done. In my previous experience with JOSS, the reviewer at the time requested additional functionality to package, and it required us to cut a new release anyways.

[arokem]

Gotcha - thanks! That means that @anotherjoshsmith should go through everything else, wait until everything else is in order, and then wait for you to cut a v1.0.0 before checking that box. Is that your intention?

[cxhernandez]

Yeah, that would be great!

[anotherjoshsmith]

@cxhernandez I've submitted a short task list for JOSS acceptance as an issue. Please let me know if you have any questions or comments on these. I think you have put together a very useful research tool. I've even started testing it with data sets of my own!

[cxhernandez]

I think you have put together a very useful research tool. I've even started testing it with data sets of my own!

That's great to hear! Thanks!

I've made a PR that addresses each task item. Let me know what you think!

[anotherjoshsmith]

All review issues have been resolved.

@arokem: I suggest _"MSMExplorer: Data Visualizations for Biomolecular Dynamics"_ by @cxhernandez et al. be accepted by JOSS.

[arokem]

Thank you @anotherjoshsmith!

@cxhernandez : could you please create a Zenodo archive with the 1.0.0 version? Once you do that, I can set that as the archive, and move ahead to accept and close this issue.

[cxhernandez]

@arokem: The archive for v1.0.0 can be found here.

[arokem]

@whedon set 10.5281/zenodo.439774 as archive

[whedon]

OK. 10.5281/zenodo.439774 is the archive.

[arokem]

@arfon : I believe this one is ready to go! Anything else I need to do to get this one into this page: http://joss.theoj.org/papers/popular?

[arfon]

@arfon : I believe this one is ready to go! Anything else I need to do to get this one into this page: http://joss.theoj.org/papers/popular?

@arokem - I still have to do the last few bits. Planning on giving @whedon those super-powers sometime soon.

@arokem many thanks for editing this and @anotherjoshsmith for your review ✨

@cxhernandez - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00188 :zap: 🚀 💥