[REVIEW]: SimpleSDMLayers.jl and GBIF.jl: A Framework for Species Distribution Modeling in Julia

[whedon]

Submitting author: @gabrieldansereau (Gabriel Dansereau)
Repository: https://github.com/EcoJulia/SimpleSDMLayers.jl
Version: v0.3.4
Editor: @KristinaRiemer
Reviewer: @dglmoore, @marcjwilliams1
Archive: 10.5281/zenodo.4472905

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/7f4f28130ba9b2515909d00f82d25865/status.svg)](https://joss.theoj.org/papers/7f4f28130ba9b2515909d00f82d25865)

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

@dglmoore & @marcjwilliams1, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 @dglmoore

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@gabrieldansereau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @marcjwilliams1

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@gabrieldansereau) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

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

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dglmoore, @marcjwilliams1 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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To fix this do the following two things:

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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:

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[whedon]

👋 @dglmoore, please update us on how your review is going.

[whedon]

👋 @marcjwilliams1, please update us on how your review is going.

[marcjwilliams1]

Overall I think the package and article are excellent and they more than satisfy all the requirements for JOSS. The documentation and API is clear and easy to use and it is great to see high coverage testing (>80%) of the functionality. A few small comments below:

1. The CI is currently failing on master,I can see previous versions have been passing so have no concerns that these are important issues.
2. Although far from an expert on computational ecology I can see how this package would make some types of modeling easier through integration with other packages as mentioned in the article, are there examples of this in the wider EcoJulia ecosystem? I think it would be nice to mention if so.

[KristinaRiemer]

@marcjwilliams1 thank you for your review and your thoughtful questions/comments, hopefully @gabrieldansereau will have a chance to respond soon.

@dglmoore, I just noticed that you were not added as an assignee to this issue, I'm going to try to fix that now.

[KristinaRiemer]

@whedon re-invite @dglmoore as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[dglmoore]

@KristinaRiemer thank you for re-inviting me. I'll take care of the review today.

[dglmoore]

The article and documentation are great. The package has some really nice features that should make many common tasks painless. Performance was good and the code quality looks high.

The only concern at the moment is the failing unit tests, but I suspect that's a simple enough issue to resolve. With this possible exception, all of the JOSS requirements are met or exceeded in my opinion.

[gabrieldansereau]

@marcjwilliams1 @dglmoore Thank you for your helpful reviews and sorry for the delay.

I fixed the tests in PoisotLab/SimpleSDMLayers.jl#44 and released a new version of the package. As expected by the reviewers, it was a simple fix, a problem with the download URL for one of the supported datasets, which seems to have changed. All other functionalities should work properly.

@marcjwilliams1's comment on integration with other EcoJulia packages is very relevant, however, we do not have such an example of wider integration yet. For now, EcoJulia has a few combinations of packages working together, such as SimpleSDMLayers.jl and GBIF.jl (in review here), or Mangal.jl and EcologicalNetworks.jl (also in review at JOSS). Wider integration between more packages is a long term goal of EcoJulia, but we are not quite there yet. We will for sure include examples in the package's documentation once we do have some.

[tpoisot]

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

[KristinaRiemer]

Thanks for checking in @tpoisot. It looks like @gabrieldansereau has addressed all of the reviewer comments, so we just need final confirmation from @marcjwilliams1 and @dglmoore that they are satisfied with this submission.

[marcjwilliams1]

All good with me, can confirm I'm satisfied with this submission.

[dglmoore]

I am satisfied with the submission.

[KristinaRiemer]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[KristinaRiemer]

Thanks for the confirmations, @marcjwilliams1 & @dglmoore!

@gabrieldansereau I went through the article proof to check for reference formatting, typos, etc., and found a few things to improve:

• line 53: remove "an"
• lines 129-131: change verbs to clip, coarsen, and perform
• Chamberlain et al., 2020 should have rgbif in title lower case
• add links to software references, e.g., the suggested citation for rgbif includes link to CRAN page

You should also read through the PDF and make sure you're happy with it, let me know when you've made those updates and are done.

[gabrieldansereau]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[gabrieldansereau]

@KristinaRiemer Thank you for pointing these out.

I made the changes you requested, along with a few minor ones while re-reading. @tpoisot and I are now happy with the PDF.

[danielskatz]

In a JOSS paper, there is a single link that should point to an archive of all the reviewed software.
(This archive is a permanent record of the reviewed software, not a live version.)

In this case, the link does not - it only points to part of the reviewed software. To me, this is a problem.
But it's easy to fix, by creating an archive (in zenodo, figshare, etc.) that contains both packages - again, this is for the scholarly records associated with this paper, not for people who want to use the software, who would go to the github repos. And yes, this has to be done manually in this case, because it's not something the zenodo-github linkage supports.

[danielskatz]

ensure that the joint archive is not kept up to date, and it's not me being obtuse, I just don't see the benefits for users.

This doesn't need to be kept up to date, and it's not for users. It's for the scholarly record associated with this paper, and is a one-time need for the paper.

[tpoisot]

Is it better than linking both DOIs? I can do a one-time archive with both. if this is a requirement from the editorial board, althought I don't see the point. Just tell me which title you think it should have and I will get it done.

[danielskatz]

Linking both DOIs would be better in some ways, but the JOSS paper template doesn't support it. There is a requirement to link to the reviewed software, and I think because of the JOSS template, we need a single archive that contains it.

[tpoisot]

Here is an archive with the two zips of both packages: 10.5281/zenodo.4472905

[danielskatz]

@whedon set 10.5281/zenodo.4472905 as archive

[whedon]

OK. 10.5281/zenodo.4472905 is the archive.

[danielskatz]

hmmm - that doesn't resolve for me right now. Can you also share the direct URL for me to check?

[gabrieldansereau]

https://zenodo.org/record/4472905

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2054

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2054, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

PDF failed to compile for issue #2872 with the following error:

/app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/response/raise_error.rb:16:in on_complete': GET https://api.github.com/repos/JuliaCon/proceedings-review/issues/2872: 404 - Not Found // See: https://docs.github.com/rest/reference/issues#get-an-issue (Octokit::NotFound) from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/response.rb:9:in block in call'
from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/response.rb:61:in on_complete' from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/response.rb:8:in call'
from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/middleware/follow_redirects.rb:73:in perform_with_redirection' from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/middleware/follow_redirects.rb:61:in call'
from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/rack_builder.rb:143:in build_response' from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/connection.rb:387:in run_request'
from /app/vendor/bundle/ruby/2.6.0/gems/faraday-0.15.4/lib/faraday/connection.rb:138:in get' from /app/vendor/bundle/ruby/2.6.0/gems/sawyer-0.8.2/lib/sawyer/agent.rb:94:in call'
from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/connection.rb:156:in request' from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/connection.rb:19:in get'
from /app/vendor/bundle/ruby/2.6.0/gems/octokit-4.8.0/lib/octokit/client/issues.rb:114:in issue' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/review.rb:21:in issue_body'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:74:in compile' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in

'

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02872 joss-papers#2055
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02872
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[KristinaRiemer]

Looks like whedon was a little slow, does this need to be dealt with?

[danielskatz]

@openjournals/dev - please notice this transient problem which I worked around by just re-running the command

[danielskatz]

Congratulations to @gabrieldansereau and @tpoisot!!

And thanks to @dglmoore and @marcjwilliams1 for reviewing, and @KristinaRiemer for editing!

[whedon]

🎉🎉🎉 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.02872/status.svg)](https://doi.org/10.21105/joss.02872)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02872">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02872/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02872/status.svg
   :target: https://doi.org/10.21105/joss.02872

This is how it will look in your documentation:

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[gabrieldansereau]

Thank you very much @danielskatz @KristinaRiemer @dglmoore @marcjwilliams1!

[arfon]

Linking both DOIs would be better in some ways, but the JOSS paper template doesn't support it. There is a requirement to link to the reviewed software, and I think because of the JOSS template, we need a single archive that contains it.

👋 folks - just popping in here to say that currently this is the only way for JOSS to handle submissions like this. I would like us to be able to link to multiple software archives (and repositories) but the current model for JOSS is one review per software repository.

[KristinaRiemer]

Thanks everyone!