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[REVIEW]: FSharpGephiStreamer: An idiomatic bridge between F# and network visualization #1445

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whedon opened this issue May 13, 2019 · 14 comments

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@cgravill cgravill

@PrashantVaidyanathan PrashantVaidyanathan

@danielskatz danielskatz

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@whedon @danielskatz @cgravill @PrashantVaidyanathan
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commented May 13, 2019 •
edited by PrashantVaidyanathan

Submitting author: @muehlhaus (Timo Mühlhaus)
Repository: https://github.com/CSBiology/FSharpGephiStreamer
Version: v1.1.0
Editor: @danielskatz
Reviewer: @cgravill, @PrashantVaidyanathan
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/353e97af96ed27c448d32501fda34aed"><img src="http://joss.theoj.org/papers/353e97af96ed27c448d32501fda34aed/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/353e97af96ed27c448d32501fda34aed/status.svg)](http://joss.theoj.org/papers/353e97af96ed27c448d32501fda34aed)

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

@cgravill & @PrashantVaidyanathan, 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 @danielskatz know.

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

Review checklist for @cgravill

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 (v1.1.0)?
  • Authorship: Has the submitting author (@muehlhaus) 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 @PrashantVaidyanathan

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 (v1.1.0)?
  • Authorship: Has the submitting author (@muehlhaus) 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)?

@whedon whedon assigned danielskatz May 13, 2019

@whedon whedon added the review label May 13, 2019

@whedon whedon referenced this issue May 13, 2019

Closed

[PRE REVIEW]: FSharpGephiStreamer: An idiomatic bridge between F# and network visualization #1214

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commented May 13, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cgravill, 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 May 13, 2019 

Attempting PDF compilation. Reticulating splines etc...
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commented May 13, 2019

👉 Check article proof 📄 👈

@danielskatz danielskatz assigned cgravill May 13, 2019

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commented May 13, 2019

👋 @cgravill & @PrashantVaidyanathan - thanks for agreeing to review.

Please carry out your review in this issue by updating your checklist above. The checklist gives me some insight into the review process and any blocking issues, as well as being the full set of items that once passed will lead us to accept the submission.

And please fully read the the top 2 comments in this issue. If you have any problems or questions, please feel free to let me know.

@danielskatz danielskatz unassigned cgravill and danielskatz May 13, 2019

@whedon whedon assigned cgravill, danielskatz and PrashantVaidyanathan May 14, 2019

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commented May 18, 2019

👋 @cgravill & @PrashantVaidyanathan - Is there anything I can do to help with your reviews?

If you can at least check your "Conflict of interest" and "Code of Conduct" boxes when you feel ready, that would help me know that the processes are working and that you are starting :)

(And @PrashantVaidyanathan, yes, I do remember that you will not be working on this 'till next week due to travel)
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commented May 18, 2019 •
edited

Sure, completed those steps @danielskatz

How precisely should these requirements be taken? For example, they have a plain text license but it includes a .txt extension. Is that OK?

https://joss.readthedocs.io/en/latest/review_criteria.html#software-license
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commented May 18, 2019

You could ask that this be changed to have no extension, since the JOSS criteria says "Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?" and since the GitHub guidance for this is for it to either have no extension or be .md. You could open an issue in the software repo to request this, and put in a comment here pointing to that issue.

@cgravill cgravill referenced this issue May 18, 2019

Closed

REVIEW: license file naming #8

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commented May 18, 2019

I'm not aware it's a conflict of interest but for full transparency:
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commented May 18, 2019

@PrashantVaidyanathan and I are both employed in a group at the same institution: Microsoft Research

Are you both employed in the same group? Do you work together on the same projects?

I'm also a contributor to https://github.com/Microsoft/automatic-graph-layout an alternative network library to Gephi, and tools to connect to it from F#

Expertise in the subject is good.

With both factors in mind, do you feel that you can provide a fair and unbiased review and advise?
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commented May 18, 2019

Yes, we're both employed in this group https://www.microsoft.com/en-us/research/group/biological-computation/ and have overlap in projects.

We've not discussed the contents of this work.

I feel I'm able to give a fair and unbiased review.

This was referenced May 18, 2019

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commented May 19, 2019

Thanks for providing this info, @cgravill

Given the particular circumstances of this software and this conflict, we (the associate editors-in-chief) have decided that we will note it and waive it for this review. So please continue the review.
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commented May 23, 2019

👋 @PrashantVaidyanathan - have you had a chance to start looking at this yet?
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commented May 24, 2019

@danielskatz Apologies for the delay. I had spotty net connection over the last few days while travelling. I've started reviewing the submission now.

This was referenced Jun 1, 2019

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commented Jun 3, 2019

It looks like there are some issues being worked through, which is good - @muehlhaus and @cgravill and @PrashantVaidyanathan, please let me know if anything seems to get stuck
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