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[REVIEW]: JCOL: A Java package for solving the graph coloring problem #1843

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whedon opened this issue Oct 29, 2019 · 17 comments
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@whedon whedon commented Oct 29, 2019 •
edited by HaoZeke

Submitting author: @shah314 (Shalin S Shah)
Repository: https://github.com/shah314/graphcoloring
Version: v1.1
Editor: @jedbrown
Reviewers: @HaoZeke, @ProbShin
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/07cf7b3c7dc9037ad19f0b2ae81cde14"><img src="https://joss.theoj.org/papers/07cf7b3c7dc9037ad19f0b2ae81cde14/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/07cf7b3c7dc9037ad19f0b2ae81cde14/status.svg)](https://joss.theoj.org/papers/07cf7b3c7dc9037ad19f0b2ae81cde14)

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

@HaoZeke and @ProbShin, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jedbrown know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @HaoZeke

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@shah314) 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @ProbShin

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@shah314) 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
@whedon whedon added the review label Oct 29, 2019
@whedon whedon mentioned this issue Oct 29, 2019
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@whedon whedon commented Oct 29, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @HaoZeke it looks like you're currently assigned to review 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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@whedon whedon commented Oct 29, 2019 

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 29, 2019

👉 Check article proof 📄 👈

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@jedbrown jedbrown commented Oct 29, 2019 •
edited

👋🏼 @HaoZeke @ProbShin Welcome and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the GraphColoring repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/1843 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.
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@jedbrown jedbrown commented Oct 30, 2019

@whedon add ProbShin as reviewer
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@whedon whedon commented Oct 30, 2019

OK, ProbShin is now a reviewer
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@jedbrown jedbrown commented Oct 30, 2019

👋 @ProbShin Welcome, and thanks for agreeing to review! Please have a look at the instructions above and let me know if you have questions.
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@shah314 shah314 commented Nov 20, 2019

@jedbrown Can I change the name of the paper?
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@jedbrown jedbrown commented Nov 20, 2019

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@shah314 shah314 commented Nov 20, 2019

@whedon generate pdf
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@whedon whedon commented Nov 20, 2019 

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 20, 2019

👉 Check article proof 📄 👈

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@shah314 shah314 commented Nov 20, 2019

@jedbrown I have changed the name in the paper to the following:

JCOL: A Java package for solving the graph coloring problem
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@shah314 shah314 commented Nov 20, 2019

@whedon commands
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@whedon whedon commented Nov 20, 2019

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

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references
@jedbrown jedbrown changed the title [REVIEW]: GraphColoring: A Java package for solving the graph coloring problem [REVIEW]: JCOL: A Java package for solving the graph coloring problem Nov 21, 2019
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@danielskatz danielskatz commented Dec 5, 2019

👋 @jedbrown - just checking in on the status of this review...
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@jedbrown jedbrown commented Dec 5, 2019

@ProbShin @HaoZeke 👋 How is your review going? Is there anything we can do to assist?
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