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

whedon commented 4 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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Status

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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:

Make sure you're logged in to your GitHub account
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

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@FrancisBanville) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @arbennett

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@FrancisBanville) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

KristinaRiemer commented 3 years ago

That looks great, thanks for doing that!

The next steps are to: 1) generate a new tagged release on GitHub and 2) archive the code (on Zenodo, figshare, institutional repository, etc.) to generate a DOI. If you can post the tag version and a link to the DOI here when you're done please.

FrancisBanville commented 3 years ago

Hello @KristinaRiemer, The tagged versions are v0.4.3 for EcologicalNetworks.jl and v0.3.1 for Mangal.jl. We archived our repositories and the code to reproduce our paper on Zenodo at this link.

Please let me know if everything is okay. Thank you!

KristinaRiemer commented 3 years ago

Great, I'll use the EcologicalNetworks version here. Could you change the Zenodo title to match the software paper title?

KristinaRiemer commented 3 years ago

@whedon set v0.4.3 as version

whedon commented 3 years ago

OK. v0.4.3 is the version.

tpoisot commented 3 years ago

Hi @KristinaRiemer - is there a thing we need to do at this point?

KristinaRiemer commented 3 years ago

Oh, sorry, I didn't see that the Zenodo title was changed! Thanks for doing that @FrancisBanville.

KristinaRiemer commented 3 years ago

@whedon set 10.5281/zenodo.4716483 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4716483 is the archive.

KristinaRiemer commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

 Can't find any papers to compile :-(

KristinaRiemer commented 3 years ago

@whedon accept from branch joss-article-review1

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

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

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2279

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2279, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-article-review1

tpoisot commented 3 years ago

Proofs are :+1:

KristinaRiemer commented 3 years ago

For the last step, an EiC will do the final approval, and then it will be published!

kthyng commented 3 years ago

looks good!

kthyng commented 3 years ago

@whedon accept deposit=true from branch joss-article-review1

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2280
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02721
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

Congrats on your new publication @FrancisBanville! Many thanks to editor @KristinaRiemer and reviewers @kellykochanski and @arbennett for your time, hard work, and expertise!!

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02721/status.svg)](https://doi.org/10.21105/joss.02721)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02721">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02721/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02721/status.svg
   :target: https://doi.org/10.21105/joss.02721

This is how it will look in your documentation:

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FrancisBanville commented 3 years ago

Great, thank you so much @kthyng, @KristinaRiemer, @kellykochanski, and @arbennett for your time and useful comments! 🎉

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