[PRE REVIEW]: Netgraph: Publication-quality Network Visualisations in Python

[editorialbot]

Submitting author: !--author-handle-->@paulbrodersen<!--end-author-handle-- (Paul Brodersen) Repository: https://github.com/paulbrodersen/netgraph/ Branch with paper.md (empty if default branch): joss Version: 4.12.4 Editor: !--editor-->@rkurchin<!--end-editor-- Reviewers: @jonjoncardoso, @ortega2247 Managing EiC: Daniel S. Katz

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Author instructions

Thanks for submitting your paper to JOSS @paulbrodersen. Currently, there isn't a JOSS editor assigned to your paper.

@paulbrodersen if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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[editorialbot]

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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

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[editorialbot]

Couldn't check the bibtex because branch name is incorrect: https://github.com/paulbrodersen/netgraph/tree/joss/publication

[editorialbot]

Couldn't check the bibtex because branch name is incorrect: https://github.com/paulbrodersen/netgraph/tree/joss/publication

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

@editorialbot set joss as branch

[editorialbot]

Done! branch is now joss

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.72 s (160.7 files/s, 173470.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4            118          95014
Python                          43           2159           3416           5190
Markdown                         2             97              0            311
reStructuredText                37           1750          14034            307
TeX                              1              0              0             74
Jupyter Notebook                23              0           1405             56
TOML                             1              4              0             51
YAML                             2              6             18             32
DOS Batch                        1              8              1             26
make                             1              4              7              9
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SUM:                           115           4032          18999         101070
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 441

[danielskatz]

@editorialbot check references

[danielskatz]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.6084/m9.figshare.1164194 is OK
- 10.1101/gr.1239303 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- 10.1007/3-540-45848-4_57 may be a valid DOI for title: Graphviz— Open Source Graph Drawing Tools
- 10.1609/icwsm.v3i1.13937 may be a valid DOI for title: Gephi: An Open Source Software for Exploring and Manipulating Networks

INVALID DOIs

- None

[danielskatz]

👋 @paulbrodersen - thanks for your submission. There are a couple of issues:

1. Note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

2. I'm going to start a scope review amongst the JOSS editors to decide if this submission is research software as defined by JOSS. This does not mean that it is not software that is useful in research, but just that JOSS might not consider it in scope for review as research software. In particular, visualization software that does not also do some analysis is often considered out of scope.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[paulbrodersen]

@editorialbot check references

[paulbrodersen]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.6084/m9.figshare.1164194 is OK
- 10.1007/3-540-45848-4_57 is OK
- 10.1101/gr.1239303 is OK
- 10.1609/icwsm.v3i1.13937 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[paulbrodersen]

@editorialbot generate pdf

[editorialbot]

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

[paulbrodersen]

@danielskatz

Thanks for lightening fast editorial review. With respect to the raised issues:

Note that your paper does not compile.

I have fixed a typo (affilitations -> affiliations) and the paper does now compile.

In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect.

I have checked the doi suggestions by your editorialbot and they are correct according to doi.org. I have amended the bibtex file accordingly.

I'm going to start a scope review amongst the JOSS editors to decide if this submission is research software as defined by JOSS.

If I may ever so briefly argue my case: graph drawing and network visualisation are a niche but an active area of research with yearly conferences and the occasional special issue in respected academic journals. Netgraph specifically implements several graph drawing algorithms for which no other open source implementation is available, e.g. the edge bundling algorithm by Holten & Wijk (2009). As such, netgraph is not only a visualisation tool but can also serve as a reference for future research in related methods and thus makes an important contribution to the field.

[paulbrodersen]

Regarding potential reviewers, my preferred choices would be tacaswell and/or briatte. Netgraph builds on matplotlib, and tacaswell (matplotlib's lead maintainer) is aware of my work as he has helped me with particularly gnarly issues in the past. briatte has authored a very similar library (ggnetwork) for the R programming language, and would hence be in a unique position to judge the merits of this work.

Based on the linked table, the following people also seem highly suitable given that their preferred programming language includes python, and their domains of expertise include network analysis or network science and visualisation. However, I am unfamiliar with their work (or at least their github handle).

• jankatins
• alexanderfurnas
• adavidzh
• camillescott
• ortega2247
• tomalrussell
• jkbren

[danielskatz]

Thanks @paulbrodersen - let's see what the editors think, then perhaps we can proceed with some of your reviewers suggestions - again, this will be about a week until there's a next step.

[rkurchin]

If this passes scope query, I'm happy to edit it!

[danielskatz]

Thanks @rkurchin - I'm going to assign this to you, as it has passed the scope query

[danielskatz]

@editorialbot assign @rkurchin as editor

[editorialbot]

Assigned! @rkurchin is now the editor

[paulbrodersen]

Thank you, that is great news!

[rkurchin]

👋 @jonjoncardoso and @jkbren, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[jonjoncardoso]

Yes, count me in!

[rkurchin]

@editorialbot add @jonjoncardoso as reviewer

[editorialbot]

@jonjoncardoso added to the reviewers list!

[rkurchin]

👋 @camillescott, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[danielskatz]

👋 @rkurchin - How are you doing on looking for reviewers?

[rkurchin]

@adavidzh, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

(@danielskatz, sorry for delay here – my wedding was this past weekend, so there were a few other things on my mind 🤪 )

[paulbrodersen]

@rkurchin Congratulations, and I hope you made good memories.

[adavidzh]

@adavidzh, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I am not able to commit the time to take this through right now. I did take a cursory look at the repository and I could not identify community guidelines.

(@danielskatz, sorry for delay here – my wedding was this past weekend, so there were a few other things on my mind 🤪 )

Congratulations!

[rkurchin]

👋 @ortega2247 and/or @tomalrussell, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[jonjoncardoso]

Hi,

I am still happy to do the review. However, I underestimated the time I’d have before the Easter Break. I’m travelling right now and I’ll only be able to do so in early may. If that’s not a problem, or if you can’t find alternative reviewers, I can still review by then.

On Sun, 9 Apr 2023 at 16:23, Rachel Kurchin @.***> wrote:

👋 @ortega2247 https://github.com/ortega2247 and/or @tomalrussell https://github.com/tomalrussell, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5264#issuecomment-1501196265, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG2Z7VBDUXVVDVXSPBUG53XAMEBLANCNFSM6AAAAAAV5MUJIU . You are receiving this because you were assigned.Message ID: @.***>

-- Jonathan Cardoso-Silva, PhD Data Science Institute/Department of Methodology London School of Economics and Political Science

[rkurchin]

@jonjoncardoso, that's fine, thanks for letting me know. As soon as we find another reviewer or two, the review issue will open and there will be instructions there for how to proceed.

[paulbrodersen]

@adavidzh Hi, thanks for checking out my project. You are correct that I don't have a section that is titled "Community Guidelines". I do, however, have the following paragraphs that serve the same purpose under the heading "Contributing & Support" on ReadTheDocs and under "Help, I don't know how to do ..." on the Github README:

---

If you get stuck, please raise an issue on Github. Include any relevant code and data in a minimal, reproducible example. If applicable, make a sketch of the desired result with pen and paper, take a picture, and append it to the issue. Bug reports are, of course, always welcome. Please make sure to include the full error trace. If you submit a pull request that fixes a bug or implements a cool feature, I will probably worship the ground you walk on for the rest of the week. Probably.

---

If there is anything missing to qualify as "Community Guidelines" or if you have any other suggestions for improvements, then I would love to hear them.

[tomalrussell]

Hi @rkurchin - yes, I'll be happy to review this.

[paulbrodersen]

@rkurchin: Before @tomalrussell puts any work into this, I just wanted to double-check what JOSS' conflicts of interest policy says about the reviewer and reviewee being from the same university? @tomalrussell and I have never met (as far as I know) and we work in different departments but I noticed on his github profile that we are both at Oxford. If that is fine with JOSS, I would love to have him as a reviewer (at least so far ;-)).

[tomalrussell]

double-check what JOSS' conflicts of interest policy says about the reviewer and reviewee being from the same university

Ah, good catch @paulbrodersen - https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy does flag this case. Hopefully this can be noted and waived as we are "both employed by the same very large organization but in different units without any knowledge of each other." (I'm over in Geography, and I don't believe we've met - yet!)

[rkurchin]

Thanks for flagging this – I agree that this sounds like a reasonably clear case for the waiver, but I'm going to double-check with the @openjournals/csism-eics team just to make sure!

[danielskatz]

@rkurchin - if you can find another reviewer, please do. It doesn't seem like this work is so narrowly-focused that we need to choose a reviewer with a COI and then waive it.

[rkurchin]

👋 @jankatins and/or @alexanderfurnas, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[ortega2247]

I would be happy to review this paper