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[REVIEW]: Agents.jl: agent-based modeling framework in Julia #1611

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whedon opened this issue Jul 30, 2019 · 72 comments

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commented Jul 30, 2019

Submitting author: @kavir1698 (Ali Rezaee Vahdati)
Repository: https://github.com/kavir1698/Agents.jl
Version: v1.1.8
Editor: @jedbrown
Reviewers: @Datseris, @mozhgan-kch
Archive: 10.5281/zenodo.3477581

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/11ec21a6bb0a6e9992c07f26a601d580"><img src="http://joss.theoj.org/papers/11ec21a6bb0a6e9992c07f26a601d580/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/11ec21a6bb0a6e9992c07f26a601d580/status.svg)](http://joss.theoj.org/papers/11ec21a6bb0a6e9992c07f26a601d580)

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

@Datseris and @mozhgan-kch, 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 @Datseris

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: v1.1.8
  • Authorship: Has the submitting author (@kavir1698) 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 @mozhgan-kch

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: v1.1.8
  • Authorship: Has the submitting author (@kavir1698) 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

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commented Jul 30, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Datseris 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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commented Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 30, 2019

@jedbrown

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commented Jul 30, 2019

@Datseris 👋 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 Agents.jl repository). I'll be watching this thread if you have any questions.

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commented Jul 30, 2019

Below is my review comments. Items beginning with [OPTIONAL] are up to the author to tackle and I am happy to accept publication even without them implemented. For the rest, I require them to be finalized for me to accept publication.

(this list is updated as the review progresses)

  • The currently installed version for the package manager is 1.1.0. This does not match the submitted version of 1.1.2. Regardless, I think a new version should be associated with the paper anyways, one that includes the bugfixes stemming from this review.
  • A claim of performance is not made directly per se, but the author uses the known fact that Julia is faster than Python and provides a comparison graph in the paper. The caption of the graph then points to the docs. But in the (stable version of) the docs, I could not find more details on the performance graph. I think for transparency both the Julia and Python scripts that were used to produce the graph should be available in the documentation.
  • [OPTIONAL] possible documentation improvements: JuliaDynamics/Agents.jl#16
  • 2 out of 4 References do not have a DOI. (But I don't know if the actual papers have a DOI either)
  • It seems that the paper lacks scientific introduction and motivation. I'd recommend to include the opening paragraph of the documentation (of the dev documentation) into the paper.
  • Solve JuliaDynamics/Agents.jl#21
  • Solve JuliaDynamics/Agents.jl#22
@Datseris

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commented Aug 2, 2019

@jedbrown @kavir1698 I think I have now finished the first round of review. The above checklist states what I feel should be taken care of before acceptance.

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commented Aug 9, 2019

@whedon generate pdf

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commented Aug 9, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Aug 9, 2019

@kavir1698

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commented Aug 9, 2019

Thank you, @Datseris, for your review.

@jedbrown I have released a new version (v1.1.7) for the package. I do not know how to change the version in the paper, though.

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commented Aug 9, 2019

@whedon set v1.1.7 as version

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commented Aug 9, 2019

OK. v1.1.7 is the version.

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commented Aug 9, 2019

Please notice that for my review to conclude, a new version of the software should be released in the Julia package ecosystem. That will correspond to the version a user would obtain via normal installation, pkg> add Agents. Although this seems a technicality, it is nevertheless the way a Julia package is installed (unless one wants to mess with the master branch, where versions do not really matter).

I recommend @kavir1698 to leverage JuliaRegistrator as instructed here: JuliaDynamics/Agents.jl#25

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commented Aug 14, 2019

Hi @Datseris, v1.1.7 is now released in the Julia package ecosystem.

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commented Aug 14, 2019

Great! @jedbrown I conclude my review now. All points pass in my eyes.

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commented Aug 16, 2019

Thanks, @Datseris!
@kavir1698, thanks for your patience, I'll add a second reviewer now.

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commented Aug 16, 2019

@whedon add @mozhgan-kch as reviewer

@whedon whedon assigned Datseris and jedbrown and unassigned jedbrown and Datseris Aug 16, 2019
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commented Aug 16, 2019

OK, @mozhgan-kch is now a reviewer

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commented Aug 16, 2019

@mozhgan-kch 👋 Welcome, and thanks for agreeing to review! The comments from @whedon at the top of this thread outline the review process, which takes place in this thread (possibly with issues filed in the Agents.jl repository). There is a review checklist for you above. I'll be watching this thread if you have any questions.

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commented Sep 11, 2019

@jedbrown @mozhgan-kch this review has been a bit stale for >3 weeks. Can you give an estimate of when the review process will be completed?
@mozhgan-kch thanks for your help with this review. Please let us know when you feel you can finalize this review process? If you need more time please let us know as well. Thanks.

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commented Sep 13, 2019

Hi @Kevin-Mattheus-Moerman @jedbrown, I would need extra time for this as I was away on leave and will be in only this week. I'll try to sort this out next week. Cheers.

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commented Oct 8, 2019

OK. v1.1.8 is the version.

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commented Oct 8, 2019

@whedon set 10.5281/zenodo.3477581 as archive

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commented Oct 8, 2019

OK. 10.5281/zenodo.3477581 is the archive.

@kavir1698

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commented Oct 8, 2019

The author list is updated.

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commented Oct 8, 2019

@whedon accept

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commented Oct 8, 2019

Attempting dry run of processing paper acceptance...
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commented Oct 8, 2019


OK DOIs

- 10.1038/460685a is OK
- 10.1016/j.ecolmodel.2006.04.023 is OK
- 10.1177/0037549705058073 is OK
- 10.25080/majora-7b98e3ed-009 is OK
- 10.1186/2194-3206-1-3 is OK
- 10.1073/pnas.082080899 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Oct 8, 2019

Check final proof 👉 openjournals/joss-papers#1012

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1012, 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 Oct 8, 2019

Thanks, @kavir1698. Over to you, @openjournals/joss-eics.

@jedbrown jedbrown added the accepted label Oct 8, 2019
@kavir1698

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commented Oct 8, 2019

Thank you, @jedbrown.

@Datseris

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commented Oct 8, 2019

@kavir1698 congratulations!

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commented Oct 8, 2019

Thank you very much, @Datseris

@labarba

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commented Oct 8, 2019

@kavir1698 — could you edit the metadata of the Zenodo deposit so the title matches the paper?

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commented Oct 8, 2019

@labarba, the title is updated.

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commented Oct 8, 2019

I jus finished reading the paper—all good, except for the performance comparison in Figure 1, it would be nice if you provided the specs of the hardware used for the test!

@kavir1698

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commented Oct 8, 2019

I have added the following line to the figure caption:

"The comparison was performed on a Windows machine with a i7-6500U CPU and 16 GB of RAM."

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commented Oct 8, 2019

@whedon accept deposit=true

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commented Oct 8, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Oct 8, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Oct 8, 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#1014
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01611
  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 Oct 8, 2019

Congratulations, @kavir1698, your JOSS paper is now published! 🚀

Huge thanks to our editor: @jedbrown, and the reviewers: @Datseris, @mozhgan-kch — your contribution to JOSS is much appreciated 🙏

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commented Oct 8, 2019

Thank you all.

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commented Oct 8, 2019

@arfon — I just looked at the PDF, and it doesn't contain the last commit by the author. Is @whedon not able to catch a very recent commit?

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commented Oct 8, 2019

@labarba @arfon could the issue be that the change was made after the initial whedon accept command, and then whedon used that version with the deposit?

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commented Oct 8, 2019

I don't think so. In another paper I just published, some copy edits I submitted via PR did not appear in the PDF doing a @whedon accept immediately after the merge, but after waiting a while, I ran it again, and they got caught.I have a feeling there's some caching delay or whatnot.

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commented Oct 8, 2019

Here I did @whedon accept deposit=true too quick, I'm afraid...

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commented Oct 9, 2019

I just regenerated the PDF locally and updated the joss-papers repo with the new PDF.

This is showing up as fixed for me now but might take a few hours to show up as modified for some of you as there's caching in place for the PDFs.

@labarba labarba closed this Oct 9, 2019
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commented Oct 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](https://joss.theoj.org/papers/10.21105/joss.01611/status.svg)](https://doi.org/10.21105/joss.01611)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01611">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01611/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01611/status.svg
   :target: https://doi.org/10.21105/joss.01611

This is how it will look in your documentation:

DOI

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