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[REVIEW]: EoN (Epidemics on Networks), software for simulation, analytic approximation, and analysis of epidemics on networks #1731

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whedon opened this issue Sep 15, 2019 · 107 comments
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@whedon whedon commented Sep 15, 2019

Submitting author: @joelmiller (Joel Miller)
Repository: https://github.com/springer-math/Mathematics-of-Epidemics-on-Networks
Version: v1.1
Editor: @lpantano
Reviewers: @acolum, @pholme, @hagberg
Archive: 10.5281/zenodo.3572756

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d00ea63dc7a7c56cf73852229031b8f5"><img src="https://joss.theoj.org/papers/d00ea63dc7a7c56cf73852229031b8f5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d00ea63dc7a7c56cf73852229031b8f5/status.svg)](https://joss.theoj.org/papers/d00ea63dc7a7c56cf73852229031b8f5)

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

@acolum & @pholme, 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 @lpantano know.

Please try and complete your review in the next two weeks

Review checklist for @acolum

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?
  • Contribution and authorship: Has the submitting author (@joelmiller) 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 @pholme

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?
  • Contribution and authorship: Has the submitting author (@joelmiller) 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 @hagberg

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?
  • Contribution and authorship: Has the submitting author (@joelmiller) 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?
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@whedon whedon commented Sep 15, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @acolum, @pholme 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 Sep 15, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Sep 15, 2019

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@acolum acolum commented Sep 24, 2019

Just finished my review - everything looks great!

@lpantano

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@lpantano lpantano commented Oct 3, 2019

Thank you @acolum! 👋 @pholme let me know if you need something else to complete the review.

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@lpantano lpantano commented Oct 18, 2019

👋 @pholme, are you still able to review this? Let me know.

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@lpantano lpantano commented Oct 23, 2019

@whedon add @hagberg as reviewer

@whedon whedon assigned acolum and lpantano and unassigned lpantano and acolum Oct 23, 2019
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@whedon whedon commented Oct 23, 2019

OK, @hagberg is now a reviewer

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@lpantano lpantano commented Nov 11, 2019

@hagberg how is the review going?

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@lpantano lpantano commented Nov 25, 2019

Hi @hagberg, did you end up opening the issues to ask the authors to change issues you saw during the review? If yes, can you link them here? Thanks!

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@joelmiller joelmiller commented Dec 3, 2019

@whedon generate pdf

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@whedon whedon commented Dec 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 3, 2019

PDF failed to compile for issue #1731 with the following error:

Error reading bibliography ./paper.bib (line 39, column 1):
unexpected "y"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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@joelmiller joelmiller commented Dec 3, 2019

@whedon generate pdf

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@whedon whedon commented Dec 3, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 3, 2019

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@joelmiller joelmiller commented Dec 3, 2019

Hi @lpantano - Do you know if there is any way to embed a video into the pdf file? One of the final things I want to show is a tool to build an animation, but at present I can't find any way to embed it.

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@joelmiller joelmiller commented Dec 4, 2019

@hagberg

I've added the functional testing (created by @tinghf ) into the repository under EoN/tests

I've also added a discussion of related packages into the paper.

Let me know of anything else you'd like improved.

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@hagberg hagberg commented Dec 5, 2019

Looks good. Issues are closed.

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@whedon whedon commented Dec 18, 2019

Check final proof 👉 openjournals/joss-papers#1186

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1186, 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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@arfon arfon commented Dec 18, 2019

@lpantano @joelmiller - this paper is very long for JOSS (24 pages). From a quick review, there look to been a substantial amount of documentation (e.g. code examples) that would be more appropriate in supporting documentation.

What do you think about moving this content into the docs?

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@labarba labarba commented Dec 18, 2019

In fact, the JOSS documentation stipulates that papers should be short: "The paper should be between 250-1000 words." And also,

a “full length” paper is not permitted, and software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

TL;DR: JOSS does not publish long-form papers.

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@joelmiller joelmiller commented Dec 19, 2019

@whedon generate pdf

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@whedon whedon commented Dec 19, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 19, 2019

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@joelmiller joelmiller commented Dec 19, 2019

@whedon generate pdf

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@whedon whedon commented Dec 19, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 19, 2019

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@joelmiller joelmiller commented Dec 19, 2019

@whedon generate pdf

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@whedon whedon commented Dec 19, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 19, 2019

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@joelmiller joelmiller commented Dec 19, 2019

@lpantano @arfon @labarba I've dramatically shortened the paper. Please let me know if there are any further concerns.

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@joelmiller joelmiller commented Dec 19, 2019

@whedon check references

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@whedon whedon commented Dec 19, 2019

Attempting to check references...
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@whedon whedon commented Dec 19, 2019


OK DOIs

- 10.1016/j.physa.2006.06.018 is OK
- 10.1016/j.cpc.2017.06.007 is OK
- 10.1103/PhysRevE.96.022301 is OK
- 10.1090/S0002-9947-1945-0013857-4 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1021/j100540a008 is OK
- 10.1103/PhysRevE.93.042316 is OK
- 10.25080/issn.2575-9752 is OK
- 10.1007/978-3-319-50806-1 is OK
- 10.1063/1.5010002 is OK
- 10.1103/PhysRevE.87.060801 is OK
- 10.1093/comnet/cnv021 is OK
- 10.1098/rsif.2011.0403 is OK
- 10.1103/PhysRevE.80.020901 is OK
- 10.1093/bioinformatics/bty921 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.103.058701 is OK
- 10.1186/s13362-019-0058-7 is OK
- 10.1073/pnas.082090499 is OK
- 10.1086/jar.33.4.3629752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@labarba labarba commented Dec 19, 2019

Could you merge some minor copy edits, here? springer-math/Mathematics-of-Epidemics-on-Networks#47

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@joelmiller joelmiller commented Dec 20, 2019

merged

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@labarba labarba commented Dec 20, 2019

@whedon accept

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@whedon whedon commented Dec 20, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 20, 2019


OK DOIs

- 10.1016/j.physa.2006.06.018 is OK
- 10.1016/j.cpc.2017.06.007 is OK
- 10.1103/PhysRevE.96.022301 is OK
- 10.1090/S0002-9947-1945-0013857-4 is OK
- 10.18637/jss.v084.i08 is OK
- 10.1021/j100540a008 is OK
- 10.1103/PhysRevE.93.042316 is OK
- 10.25080/issn.2575-9752 is OK
- 10.1007/978-3-319-50806-1 is OK
- 10.1063/1.5010002 is OK
- 10.1103/PhysRevE.87.060801 is OK
- 10.1093/comnet/cnv021 is OK
- 10.1098/rsif.2011.0403 is OK
- 10.1103/PhysRevE.80.020901 is OK
- 10.1093/bioinformatics/bty921 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.103.058701 is OK
- 10.1186/s13362-019-0058-7 is OK
- 10.1073/pnas.082090499 is OK
- 10.1086/jar.33.4.3629752 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 20, 2019

Check final proof 👉 openjournals/joss-papers#1196

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1196, 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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@labarba labarba commented Dec 20, 2019

@whedon accept deposit=true

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@whedon whedon commented Dec 20, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Dec 20, 2019
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@whedon whedon commented Dec 20, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Dec 20, 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#1197
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01731
  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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@labarba labarba commented Dec 20, 2019

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

Huge thanks to our editor: @lpantano, and the reviewers: @acolum, @pholme, @hagberg — we couldn't do this without you and we are grateful 🙏

@labarba labarba closed this Dec 20, 2019
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@whedon whedon commented Dec 20, 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](https://joss.theoj.org/papers/10.21105/joss.01731/status.svg)](https://doi.org/10.21105/joss.01731)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01731">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01731/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01731/status.svg
   :target: https://doi.org/10.21105/joss.01731

This is how it will look in your documentation:

DOI

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