Joss-reviews: [PRE REVIEW]: Mangal.jl and EcologicalNetworks.jl: Two complementary packages for analyzing ecological networks in Julia

[whedon]

Submitting author: @FrancisBanville (Francis Banville)
Repository: https://github.com/EcoJulia/EcologicalNetworks.jl
Version: v0.3.0
Editor: @KristinaRiemer
Reviewers: @kellykochanski, @arbennett
Managing EiC: Kyle Niemeyer

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

The author's suggestion for the handling editor is @KristinaRiemer.

@FrancisBanville 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

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.13 s (377.5 files/s, 16585.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           26            206             43            861
Markdown                        15            277              0            579
YAML                             5              9              0            103
TOML                             2              5              0             26
-------------------------------------------------------------------------------
SUM:                            48            497             43           1569
-------------------------------------------------------------------------------


Statistical information for the repository '2680' was gathered on 2020/09/17.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #2680 with the following error:

Can't find any papers to compile :-(

[kyleniemeyer]

@whedon generate pdf from branch joss-manuscript

[whedon]

Attempting PDF compilation from custom branch joss-manuscript. Reticulating splines etc...

[whedon]

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

[kyleniemeyer]

Hi @FrancisBanville, thanks for your submission to JOSS. We'll be using this issue to assign the editor and reviewers, and also get any technical/logistical issues out of the way.

[kyleniemeyer]

@FrancisBanville one issue with your submission is that usually we only review a single software package at a time, though with some exceptions, and I think that your grouping of these two packages together does make sense.

However, you have specified Mangal.jl as the "main" repository for the submission, and your paper is in this repo. Since Mangal.jl would not actually be in the scope of JOSS by itself (as an API wrapper), we would prefer for EcologicalNetworks.jl to be the "main" repository submitted.

We can switch the software repo pointed to internally, but can you also move the paper to the EcologicalNetworks.jl repository? It is fine to live in a branch there, as it is currently in the Mangal.jl repo.

cc @arfon

[FrancisBanville]

Thank you @kyleniemeyer! The paper has been moved to the EcologicalNetworks.jl repository, in the branch joss-article.

[arfon]

Updated on our end too @kyleniemeyer

[kyleniemeyer]

@whedon generate pdf from branch joss-article

[whedon]

Attempting PDF compilation from custom branch joss-article. Reticulating splines etc...

[whedon]

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

[kyleniemeyer]

@FrancisBanville @arfon looks good, thanks!

[kyleniemeyer]

Hi @KristinaRiemer, can you edit this submission?

[kyleniemeyer]

@whedon invite @KristinaRiemer as editor

[whedon]

@KristinaRiemer has been invited to edit this submission.

[KristinaRiemer]

@kyleniemeyer I have no experience with Julia. Would it be sufficient to find two reviewers who do (and use this as a chance to introduce myself too)?

[kyleniemeyer]

@KristinaRiemer absolutely! As editor you don't really need to dive into the software itself—unless you want to!—as long as the reviewers have the appropriate expertise.

[KristinaRiemer]

I usually do poke around with the code a bit, to learn more about how other folks structure and document their software. I'll be editor for this.

[KristinaRiemer]

@whedon assign me as editor

[whedon]

OK, the editor is @KristinaRiemer

[KristinaRiemer]

@arbennett @eviatarbach @kavir1698 @kellykochanski would any of you be able and willing to review this JOSS submission?

[kellykochanski]

@KristinaRiemer sure.

[eviatarbach]

Unfortunately I cannot commit to review this one. Thank you for the invitation!

[KristinaRiemer]

Awesome, thanks @kellykochanski! And no big deal @eviatarbach, thanks for getting back about it.

This will still need a second reviewer, if @arbennett or @kavir1698 are able?

[KristinaRiemer]

@whedon assign @kellykochanski as reviewer

[whedon]

OK, @kellykochanski is now a reviewer

[arbennett]

Ah, sorry for the delay - I'd be happy to review this @KristinaRiemer!

[KristinaRiemer]

No problem at all @arbennett and thanks for being willing!

[KristinaRiemer]

@whedon add @arbennett as reviewer

[whedon]

OK, @arbennett is now a reviewer

[KristinaRiemer]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2721.

[KristinaRiemer]

@kellykochanski @arbennett the actual review will happen in the issue linked to above. Let me know there if you have questions!