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[REVIEW]: Mangal.jl and EcologicalNetworks.jl: Two complementary packages for analyzing ecological networks in Julia #2721

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @FrancisBanville (Francis Banville) Repository: https://github.com/EcoJulia/EcologicalNetworks.jl Version: v0.4.3 Editor: @KristinaRiemer Reviewer: @kellykochanski, @arbennett Archive: 10.5281/zenodo.4716483

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Markdown: [![status](https://joss.theoj.org/papers/f17d9716739dafff35e3f5f6fefdd622/status.svg)](https://joss.theoj.org/papers/f17d9716739dafff35e3f5f6fefdd622)

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

@kellykochanski & @arbennett, 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 @KristinaRiemer know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @kellykochanski

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @arbennett

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago

PDF failed to compile for issue #2721 with the following error:

Can't find any papers to compile :-(

arbennett commented 3 years ago

@FrancisBanville - it seems there's no paper in this repository to review. Is the paper in the Mangal.jl repo?

FrancisBanville commented 3 years ago

@arbennett - The paper is in the branch joss-article of the EcologicalNetworks.jl repository.

Sorry for the confusion!

kellykochanski commented 3 years ago

@KristinaRiemer I can't edit the checklist (despite logging in and accepting the invitation, as suggested) - can you make sure I'm added?

kellykochanski commented 3 years ago

@whedon generate pdf from branch joss-article

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-article. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kellykochanski commented 3 years ago

@KristinaRiemer I still can't edit the checklist - either I'm missing something simple or it's a bug. I'm definitely logged in, I did accept the invitation (although if I click the link now, it's no longer available - says either the invitation was revoked or I'm in the wrong account?). I've tried both chrome and firefox.

kellykochanski commented 3 years ago

@FrancisBanville Thanks for submitting a well-written paper and test-covered code repository! I'm ready to approve you on many of the review criteria once I get the checklist working [edit: now done]. However, I am also collecting a few questions and issues. These are raised on your repository as issues 166-168:

I'm aiming to raise small issues, each relating to one or more specific JOSS review criteria, to streamline the editing and approval process.

danielskatz commented 3 years ago

Let's try again

danielskatz commented 3 years ago

@whedon re-invite @kellykochanski as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@kellykochanski please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

kellykochanski commented 3 years ago

@danielskatz Thank you! It's working now.

KristinaRiemer commented 3 years ago

@danielskatz thanks for fixing that reviewer permissions problem! @kellykochanski sorry about the slow response, let me know if anything else is not working properly.

KristinaRiemer commented 3 years ago

Just checking in with reviewers @kellykochanski & @arbennett to see how everything is going and if there is anything you need help with or is blocking your progress?

FrancisBanville commented 3 years ago

@FrancisBanville Thanks for submitting a well-written paper and test-covered code repository! I'm ready to approve you on many of the review criteria once I get the checklist working [edit: now done]. However, I am also collecting a few questions and issues. These are raised on your repository as issues 166-168:

I'm aiming to raise small issues, each relating to one or more specific JOSS review criteria, to streamline the editing and approval process.

Thank you for your helpful review @kellykochanski, and sorry for the late reply!

We have made some changes to the manuscript (see branch joss-article-review1) and commented on your issues. Please do not hesitate to contact us if you have any questions or if you need further detail!

arbennett commented 3 years ago

@KristinaRiemer - sorry for the slow review. I think my review is now complete.

@FrancisBanville - thanks for this submission. The paper is well written and covers all of the required bases (I just re-looked at it in the revised branch, and also really like the added diagram). Your example use cases are very nice and prove this is robust and mature software. The code quality, from my quick, shallow dive, is really good and I like how you've described your type system hierarchy, which definitely seems to be a boon for Julia. The documentation that you've written up is also quite clean and slick, and provides both technical as well as intuitive aspects of your software design. I only have two minor considerations that I would like to see addressed before accepting this for submission. They are:

I also was unclear on the contribution and authorship question brought up by @kellykochanski - perhaps @KristinaRiemer or @danielskatz could chime in on this? To me, the response in #166 seems reasonable and I'm happy with it.

FrancisBanville commented 3 years ago

Thanks for your review @arbennett!

We changed the defective link in the revised paper (branch joss-article-review1), and included a code example in the documentation of our package. We also recently changed the look of our conceptual figure to make it slightly more attractive.

KristinaRiemer commented 3 years ago

Hi @arbennett. With regards to the authorship question, one of the authors had previously been the only contributor to the code base, while the submitting author and the third additional author had not. Based on the comments in #166 from the authors, all of their contributions seem more than sufficient for authorship as we require at JOSS. Does that make sense?

@kellykochanski it seems that the authors have addressed your feedback in #167 and #168, if you are able to follow up with those and continue your review?

Please let me know if anyone has additional questions!

arbennett commented 3 years ago

@KristinaRiemer perfect, thanks! With that, I am happy to accept this paper!

KristinaRiemer commented 3 years ago

Hi all! Hopefully everyone had a good holiday season. It looks like @arbennett has finished his review of this software. For @kellykochanski's, there are a few items left on the checklist and also two issues (167 and 168) open in the software repo. Is there anything blocking your work or anything I can do to help move this forward?

tpoisot commented 3 years ago

Hi @KristinaRiemer @kellykochanski - is there something we can do to help with the next steps?

KristinaRiemer commented 3 years ago

Thanks for following up @tpoisot. I pinged @kellykochanski via email to check in on the status of their review.

KristinaRiemer commented 3 years ago

Hi @kellykochanski, I'm not sure if I used an incorrect email address for you, just checking in on your review of this software?

tpoisot commented 3 years ago

Hi @KristinaRiemer - is there something we can do to help with the paper? Do you want suggestions for another reviewer?

KristinaRiemer commented 3 years ago

@tpoisot yes, I think at this point we should look for another reviewer. Hopefully @kellykochanski is doing alright!

If you have suggestions of reviewers with sufficient expertise that adhere to the JOSS conflict of interest guidelines, that would be great! I will also check for reviewers from our JOSS list.

tpoisot commented 3 years ago

@KristinaRiemer all the people I would think of from the top of my head have COI - but I can think about it some more.

That being said, my understanding is that @kellykochanski opened a number of issues on the repo as part of their review,

EcoJulia/EcologicalNetworks.jl#166 - contribution and authorship EcoJulia/EcologicalNetworks.jl#167 - installation instructions EcoJulia/EcologicalNetworks.jl#168 - software paper

and that @FrancisBanville addressed these comments with modifications. Could you confirm that the responses are satisfactory, and given that we've had another review with all comments resolved, can you make an editorial decision based on this?

KristinaRiemer commented 3 years ago

Hi @FrancisBanville & @tpoisot. Thank you for your patience, some folks are reaching out to see if they can get in contact with @kellykochanski.

tpoisot commented 3 years ago

Hi @KristinaRiemer - just checking-in, have you got any news? We'd like to use this paper as evidence that we are making progress on these tools for a grant, and as the submission deadline is soon, it would really help to have a decision, or comments to address in order to get closer to one.

KristinaRiemer commented 3 years ago

Hi @tpoisot. Thanks for being patient with this! We still have not been able to get in touch with @kellykochanski. So at this point, I'm going to finish out her review for her and we'll try to to wrap this up quickly, hopefully by the end of this week. Does that sound okay?

tpoisot commented 3 years ago

Perfect! Thanks a lot!!!

KristinaRiemer commented 3 years ago

Okay, I finished up the review started by @kellykochanski and everything looks good! I especially like the diagram of the package workflow in the paper. Are you leaving the paper in the joss-article-review1 branch?

Otherwise, will say this paper is accepted. We'll have a few more steps to go through, including a last review of the paper itself and getting a DOI.

KristinaRiemer commented 3 years ago

@whedon generate pdf from branch joss-article-review1

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-article-review1. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

FrancisBanville commented 3 years ago

Great, thank you @KristinaRiemer! Yes, the paper will stay in the joss-article-review1 branch for the time being.

KristinaRiemer commented 3 years ago

@whedon check references

KristinaRiemer commented 3 years ago

I'm not sure why that's not working, do I need to specify the branch there too @kyleniemeyer?

KristinaRiemer commented 3 years ago

@whedon check references from branch joss-article-review1

whedon commented 3 years ago 
Attempting to check references... from custom branch joss-article-review1
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/PhysRevE.76.066102 is OK
- 10.1073/pnas.1633576100 is OK
- 10.5281/ZENODO.889971 is OK
- 10.1111/brv.12433 is OK
- 10.1046/j.1461-0248.2002.00354.x is OK
- 10.1073/pnas.192407699 is OK
- 10.1111/2041-210X.12458 is OK
- 10.1111/j.1461-0248.2005.00868.x is OK
- 10.1146/annurev-ecolsys-012220-120819 is OK
- 10.1111/2041-210X.12005 is OK
- 10.1016/j.patter.2020.100079 is OK
- 10.1073/pnas.0601602103 is OK
- 10.1111/ecog.04310 is OK
- 10.1111/2041-210X.12468 is OK
- 10.7717/peerj.251 is OK
- 10.1038/ncomms2422 is OK
- 10.1111/jbi.12015 is OK

MISSING DOIs

- 10.1111/j.1365-2656.2010.01688.x may be a valid DOI for title: Nestedness versus Modularity in Ecological Networks: Two Sides of the Same Coin?

INVALID DOIs

- None
KristinaRiemer commented 3 years ago

Everything in the paper looks good except a couple of the references. Could you edit the Lightgraph reference so that the other contributors doesn't look like an author? And I think the DOI for the "Nestedness versus modularity in ecological networks: two sides of the same coin?" should be changed to https://doi.org/10.1111/j.1365-2656.2010.01688.x, so it doesn't show up as missing?

FrancisBanville commented 3 years ago

Thanks for pointing that out @KristinaRiemer! I fixed these two references.

KristinaRiemer commented 3 years ago

@whedon generate pdf from branch joss-article-review1

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-article-review1. Reticulating splines etc...
KristinaRiemer commented 3 years ago

@whedon check references from branch joss-article-review1

whedon commented 3 years ago 
Attempting to check references... from custom branch joss-article-review1
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/PhysRevE.76.066102 is OK
- 10.1073/pnas.1633576100 is OK
- 10.5281/ZENODO.889971 is OK
- 10.1111/brv.12433 is OK
- 10.1046/j.1461-0248.2002.00354.x is OK
- 10.1073/pnas.192407699 is OK
- 10.1111/2041-210X.12458 is OK
- 10.1111/j.1461-0248.2005.00868.x is OK
- 10.1111/j.1365-2656.2010.01688.x is OK
- 10.1146/annurev-ecolsys-012220-120819 is OK
- 10.1111/2041-210X.12005 is OK
- 10.1016/j.patter.2020.100079 is OK
- 10.1073/pnas.0601602103 is OK
- 10.1111/ecog.04310 is OK
- 10.1111/2041-210X.12468 is OK
- 10.7717/peerj.251 is OK
- 10.1038/ncomms2422 is OK
- 10.1111/jbi.12015 is OK

MISSING DOIs

- None

INVALID DOIs

- None