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[REVIEW]: WatchMe: Software for Reproducible Monitoring and Data Collection #1388

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whedon opened this issue Apr 15, 2019 · 40 comments

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commented Apr 15, 2019

Submitting author: @vsoch (Vanessa Sochat)
Repository: https://www.github.com/vsoch/watchme
Version: 0.0.13
Editor: @brainstorm
Reviewer: @andreysmelter, @crew102
Archive: 10.5281/zenodo.2633142

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/672fca0d93b6210f3d9d171e42b5a119"><img src="http://joss.theoj.org/papers/672fca0d93b6210f3d9d171e42b5a119/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/672fca0d93b6210f3d9d171e42b5a119/status.svg)](http://joss.theoj.org/papers/672fca0d93b6210f3d9d171e42b5a119)

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) by leaving comments 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

@andreysmelter and @crew102, 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 @brainstorm know.

Please try and complete your review in the next two weeks

Review checklist for @andreysmelter

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 (0.0.13)?
  • Authorship: Has the submitting author (@vsoch) 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)?

Review checklist for @crew102

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 (0.0.13)?
  • Authorship: Has the submitting author (@vsoch) 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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commented Apr 15, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @andreysmelter 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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commented Apr 15, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Apr 15, 2019

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commented Apr 15, 2019

Thanks @andreysmelter and @crew102 for offering to review, and @brainstorm for being grandmaster editor! This isn't in the paper (as it's an extra thing) but if/when you are interested, I used this tool with git hooks to show an example of how to (automatically update) some simple plots for a watcher repo -> https://vsoch.github.io/2019/watchme-git-hook/

It will make more sense after you play around a bit :)

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commented Apr 19, 2019

@brainstorm, is it OK for reviewers to make contributions to the repo they're reviewing or would that amount to some kind of conflict of interest? For example, if I see some spelling mistake in the documentation/paper, can I open a PR to fix it as part of my review?

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commented Apr 19, 2019

Why would that be a conflict of interest? I'm definitely okay with it!

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commented Apr 20, 2019

Just wanted to make sure

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commented Apr 20, 2019

@brainstorm, is it OK for reviewers to make contributions to the repo they're reviewing or would that amount to some kind of conflict of interest? For example, if I see some spelling mistake in the documentation/paper, can I open a PR to fix it as part of my review?

This is completely fine 👍

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commented Apr 20, 2019

@brainstorm , LGTM. Approved from my point of view.

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commented Apr 26, 2019

Hi @brainstorm @vsoch
I just have a quick question if I have a minor revisions/comments where do I write them? Trying to finalize review over this weekend.

Thank you.

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commented Apr 26, 2019

hey @andreysmelter this is great news!

For specific questions or edits that need to be made, what I've typically done is open up an issue for each. It might seem like overkill, but it's easier for both author and reviewer to keep track of what has been fixed, and what not. What I would likely do is reference each issue in one or more PRs to address them.

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commented Apr 26, 2019

Sounds great, @vsoch

Thank you!

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commented Apr 30, 2019

Hi @brainstorm @vsoch
I have completed my review and raised several issues that I have found against the watchme repo. They have already been fixed and merged. Everything else looks excellent to me and ready to go to the next step (acceptance/publishing?).

Thank you.

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commented May 1, 2019

@whedon check references

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commented May 1, 2019

Attempting to check references...
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commented May 1, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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commented May 4, 2019

@kyleniemeyer

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commented May 4, 2019

@whedon generate pdf

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commented May 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 4, 2019

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commented May 5, 2019

@whedon check references

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commented May 5, 2019

Attempting to check references...
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commented May 5, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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commented May 5, 2019

Doh, there are no DOIs in this paper... and after reading through this final version, looks good to me. Can you deposit the zip on Zenodo? Thx!

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commented May 5, 2019

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commented May 5, 2019

@whedon set 10.5281/zenodo.2633142 as archive

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commented May 5, 2019

OK. 10.5281/zenodo.2633142 is the archive.

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commented May 5, 2019

@kyleniemeyer @arfon I think we are done here, ready to accept imho 👍

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commented May 9, 2019

@vsoch — Could you edit the metadata of the Zenodo deposit so the title and author match the paper? Thanks!

@labarba labarba added the accepted label May 9, 2019

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commented May 9, 2019

All set!

https://zenodo.org/record/2667656#.XNQjEnVKjoo

I also added the orcid id, and license.

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commented May 9, 2019

@whedon accept

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commented May 9, 2019

Attempting dry run of processing paper acceptance...
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commented May 9, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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commented May 9, 2019

Check final proof 👉 openjournals/joss-papers#673

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#673, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented May 9, 2019

@whedon accept deposit=true

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commented May 9, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented May 9, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#674
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01388
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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commented May 9, 2019

Congratulations, @vsoch, your JOSS paper is published! 🚀

Tremendous thanks to our editor: @brainstorm, and to the reviewers: @andreysmelter, @crew102 — we appreciate all that you do 🙏

@labarba labarba closed this May 9, 2019

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commented May 9, 2019

🎉🎉🎉 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.01388/status.svg)](https://doi.org/10.21105/joss.01388)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01388">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01388/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01388/status.svg
   :target: https://doi.org/10.21105/joss.01388

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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commented May 9, 2019

Thank you @brainstorm @andreysmelter @arfon @crew102 and @labarba !

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