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[REVIEW]: js-emass: A flexible JavaScript implementation of the emass algorithm #869

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whedon opened this Issue Aug 4, 2018 · 24 comments

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whedon commented Aug 4, 2018

Submitting author: @emptyport (Michael Porter)
Repository: https://github.com/emptyport/js-emass
Version: 1.2.4
Editor: @arfon
Reviewer: @bovee
Archive: 10.5281/zenodo.1402193

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/cbc6dcaf1110a965cc8c4f1efc6a0963"><img src="http://joss.theoj.org/papers/cbc6dcaf1110a965cc8c4f1efc6a0963/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/cbc6dcaf1110a965cc8c4f1efc6a0963/status.svg)](http://joss.theoj.org/papers/cbc6dcaf1110a965cc8c4f1efc6a0963)

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 instructions & questions

@bovee, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @bovee

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (1.2.4)?
  • Authorship: Has the submitting author (@emptyport) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented Aug 4, 2018

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

⭐️ Important ⭐️

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

To fix this do the following two things:

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

watching

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

notifications

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

@whedon commands
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whedon commented Aug 4, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 4, 2018

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bovee commented Aug 7, 2018

This was a pleasure to review. Overall I think this software is a clean, well-implemented mass isotope calculator with good tests, clear API documentation and an easy installation.

I made a few small issues on the repository I'd like to see addressed and I'm not sure if this is valid as an issue on the GitHub repository itself, but expanding the second paragraph in the JOSS paper to explain how js-emass solves problems in stable isotope labeling would help sell the software and explain the need it's fulfilling.

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bovee commented Aug 7, 2018

@whedon commands

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whedon commented Aug 7, 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

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arfon commented Aug 7, 2018

This was a pleasure to review. Overall I think this software is a clean, well-implemented mass isotope calculator with good tests, clear API documentation and an easy installation.

Thanks @bovee! I notice there are a few unchecked boxes here still, are they all items that are outstanding in your mind? If so, would you mind linking to the issues you've made on the https://github.com/emptyport/js-emass repository here?

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bovee commented Aug 7, 2018

Yes, and sorry, they're all linked to issues I opened:

And I'd also like to see more elaboration on what specific problems the software solves in the paper so the "statement of purpose" is more compelling to someone who's not familiar with the original algorithm and software (but I'm not sure if that's an issue to open on the repo or not).

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emptyport commented Aug 7, 2018

@whedon generate pdf

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whedon commented Aug 7, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 7, 2018

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emptyport commented Aug 7, 2018

I just fixed a small grammatical issue with the paper and now I think everything is good.

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bovee commented Aug 7, 2018

@emptyport Thanks for those changes! And sorry, but can you explicitly link js-emass to the problem in the second paragraph? Even something like:

... can be determined by constructing a series of isotopic envelopes with js-emass ...

would go a long way towards establishing the need for this package specifically (in addition to the text you already have about why existing solutions aren't as easy-to-use).

Other than that, I think this is great and I'm ready to sign off.

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emptyport commented Aug 8, 2018

@bovee Done! Thanks for all your feedback and for helping with this submission. I never thought publishing something could be so enjoyable.

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emptyport commented Aug 22, 2018

@whedon generate pdf

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whedon commented Aug 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Aug 22, 2018

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emptyport commented Aug 22, 2018

@bovee @arfon is there anything else pending on my end?

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arfon commented Aug 22, 2018

@emptyport - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

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emptyport commented Aug 22, 2018

@arfon all done. Here is a link to the software in Zenodo and the DOI is 10.5281/zenodo.1402193

@arfon arfon added the accepted label Aug 22, 2018

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arfon commented Aug 22, 2018

@whedon set 10.5281/zenodo.1402193 as archive

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whedon commented Aug 22, 2018

OK. 10.5281/zenodo.1402193 is the archive.

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arfon commented Aug 22, 2018

@bovee - many thanks for your review here

@emptyport - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00869 ⚡️ 🚀 💥

@arfon arfon closed this Aug 22, 2018

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whedon commented Aug 22, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00869/status.svg)](https://doi.org/10.21105/joss.00869)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00869">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00869/status.svg" alt="DOI badge" >
</a>

This is how it will look in your documentation:

DOI

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