[REVIEW]: CoPro: a data-driven model for conflict risk projections

[whedon]

Submitting author: @JannisHoch (Jannis Hoch)
Repository: https://github.com/JannisHoch/copro
Version: v0.0.5
Editor: @sbenthall
Reviewer: @soodoku, @sbenthall
Archive: 10.5281/zenodo.4548904

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Review checklist for @soodoku

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 (@JannisHoch) 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 @sbenthall

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 (@JannisHoch) 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. @soodoku, @sbenthall it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

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[sbenthall]

@soodoku Sorry for the delay on starting the review. Now the review has started, and you can see the checklist on this issue.

[whedon]

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

OK DOIs

- 10.1177/0022343317691330 is OK
- 10.1177/0022343316682065 is OK
- 10.1177/0022343316682064 is OK

MISSING DOIs

- 10.1126/science.aal4483 may be a valid DOI for title: Predicting armed conflict: Time to adjust our expectations?
- 10.1088/1748-9326/11/5/054002 may be a valid DOI for title: Forecasting civil conflict along the shared socioeconomic pathways

INVALID DOIs

- None

[whedon]

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

[whedon]

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

[whedon]

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

[JannisHoch]

HI @soodoku and @sbenthall, in the meantime, the model evolved to version 0.0.6 (https://github.com/JannisHoch/copro/releases/tag/v0.0.6). All changes made in the process of this review will be committed to the branch 'joss-review' (https://github.com/JannisHoch/copro/tree/joss_review).

[soodoku]

i am done w/ my review.

[sbenthall]

I apologize for the delay in my review.
There have been some personal issues on my end that have needed extra attention.
I'm proceeding with my review now.

[sbenthall]

I think this is terribly exciting and I am eager to see it published in the best form possible. To that end:

• Please document the requirement that Conda needs to be installed to run the installation instructions.
• Is there any other comparable software that should be considered as the 'state of the field' in this line of research?
• I understand that the library has been designed for flexibility. However, I am having trouble determining from the paper and indeed from the documentation what the core functionality of the library is. I wonder if it would be possible to foreground a bit more technical detail about what scaffolding the library is doing for modeling work, and what kinds of models are included out-of-the-box.

I have not yet completed reviewing the code--these are first impressions of the document and paper only. But I think these improvements to the writeup and documentation are important for the publication.

[sbenthall]

When I get to the sh run.sh part of the instructions in the README, I get the following error:

https://gist.github.com/sbenthall/83de0ce8675283c01d3f3fa973dc6f38

[JannisHoch]

Hi @sbenthall,
Absolutely no problem!

From your comments I assume you were not looking at the most recent version of the model.
For instance, in the joss-review branch (https://github.com/JannisHoch/copro/tree/joss_review), there is no file run.sh anymore. It is renamed to 'run_notebooks.sh' for running the jupyter notebooks, and 'run_script_*.sh' for executing the command line scripts.

If your problems still occur after installing the latest copro version, please let me know. thanks :)

[JannisHoch]

in f9326d36bcbf20e93a54e6ea5733f1ae515f4477 I have added notes that the model was developed and tested with anaconda/miniconda.

[JannisHoch]

regarding your question of other state-of-the-art software: to my knowledge, there is no freely available software model with such an extensive documentation out there. of course there is model code as supplement to a publication, and publications covering similar approaches (see the references in the joss manuscript), but not in a 'structured' way like done for CoPro.

[JannisHoch]

I also have added a bit more technical detail to the JOSS manuscript. based on the review of @soodoku, the model goal and purpose were made clearer in the README and in the documentation.

[sbenthall]

Hello. Apologies for the further delay. I've had to take some family leave but am now back to work. I'll look at the branch you've referenced; sorry to miss it the first time.

[sbenthall]

I am being held up by some local Python environment issues. (The rasterio dependency is not installing properly.) I'm pretty sure this is just a problem on my end! I'll try to repair my environment setup and get back to you.

[JannisHoch]

@sbenthall, first of all, good to hear you're back!

Could you maybe attach a screenshot or so for me to look into it?

And I assume you were using the yml file to create the environment?

[sbenthall]

This is the stack trace. https://gist.github.com/sbenthall/5edad4e128fea79a99c2486ab6333bfe
Googling for it makes it look like a local python issue. I'll keep kicking at it.

[sbenthall]

Hmm.
So what's strange here is that conda install rasterio==1.1.0 works fine, but then I get an error when it installs again via pip install -e ..

I wonder if the conda version is conflicting with the pip version somehow (the pip version is invoked in the setup.py file.)

[sbenthall]

Commenting out the rasterio dependency in setup.py and rerunning the pip installation gets me this error:

https://gist.github.com/sbenthall/6a7f135970232dad08eb65ecebfd97cf

[sbenthall]

I do notice that rasterio installation instructions look like they require a number of other GDAL related packages, which in the rasterio installation instructions are listed as separate steps.

https://rasterio.readthedocs.io/en/latest/

I wonder if you could confirm that your instructions for CoPro, as written, work on a fresh system that does not have these GDAL packages installed. It is quite likely that these are being handled correctly by Anaconda and there's some issue going on locally, but if you could test on another machine that would be additional confirmation that it's a local issue and not a problem with the installation instructions.

[JannisHoch]

Hmmm, this all sounds pretty odd to me.

I have never seen any of the error messages before when installing copro - neither the one when running pip install -e . (as it seems that rasterio is correctly installed from cache and the error occurs bit later somehow), nor the one with altered setup.py file (which is a permission error after all if I get it right?).

Also, I was able to install copro (branch joss_review) on a pretty 'fresh' Linux environment.

So yes, it may be that it's a local issue. I have two ideas:

• use a different linux/windows enviroment?
• in the environment.yml file, put the rasterio dependency in the pip section instead the conda-forge section and see if this solves the suspected conflict between conda/pip?

[arfon]

@sbenthall @JannisHoch - I've updated the submission with the Zenodo archive. Next steps here are:

• Run @whedon accept from branch joss_review

Or, have @JannisHoch merge their changes into the default branch on their repository which means you then would need to run:

• @whedon accept

In both cases, the @whedon accept command will produce the final PDF proofs and notify the EiC on rotation that this submission is ready to accepted and published.

[JannisHoch]

@arfon
many thanks for fixing this.

@arfon @sbenthall
I have merged branch joss_review into default (which is dev, or does whedon choosing master as default by default?).

[arfon]

@JannisHoch - Whedon will use whatever the default is which sounds like it's dev so I think we should be good to go here.

[JannisHoch]

indeed, then we are good to go!

[sbenthall]

Thanks for your help @arfon I didn't know that about whedon and branches

[sbenthall]

@whedon accept from branch joss_review

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1146/annurev-polisci-050317-070830 is OK
- 10.1038/s41586-019-1300-6 is OK
- 10.1126/science.aal4483 is OK
- 10.1088/1748-9326/11/5/054002 is OK
- 10.1177/0022343317691330 is OK
- 10.1177/0022343316682065 is OK
- 10.1177/0022343316682064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2091

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2091, 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_review 

[sbenthall]

@whedon accept deposit=true from branch joss_review

[whedon]

I'm sorry @sbenthall, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[sbenthall]

@JannisHoch Congratulations on your acceptance. Thanks for your patience with the (long!) reviewing process.

[sbenthall]

Oh, whoops. Overstepped my authority there! I guess we have to wait for an editor-in-chief...

[JannisHoch]

@sbenthall just to inform you, I have by now merged everything into dev and removed the joss_review branch no long3r exists... But if that's leading to no issues fine by me!

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1146/annurev-polisci-050317-070830 is OK
- 10.1038/s41586-019-1300-6 is OK
- 10.1126/science.aal4483 is OK
- 10.1088/1748-9326/11/5/054002 is OK
- 10.1177/0022343317691330 is OK
- 10.1177/0022343316682065 is OK
- 10.1177/0022343316682064 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2092

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2092, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@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.02855 joss-papers#2099
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02855
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...

[arfon]

@soodoku, @sbenthall - many thanks for your reviews here and to @sbenthall for editing too! JOSS relies upon the volunteer efforts of people like you and we simply wouldn't be able to do this without you ✨

@JannisHoch - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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