[REVIEW]: MMM: A C++ library for simulating large herbivores

whedon commented 3 years ago

Submitting author: @wtraylor (Wolfgang Traylor) Repository: https://github.com/wtraylor/modular_megafauna_model Version: v1.1.3 Editor: @diehlpk Reviewers: @dirmeier, @dilawar Archive: 10.5281/zenodo.5779267

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Review checklist for @dirmeier

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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.

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General checks

[x] Repository: Is the source code for this software available at the repository url?
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[x] Contribution and authorship: Has the submitting author (@wtraylor) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @dilawar

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@wtraylor) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

whedon commented 2 years ago

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

wtraylor commented 2 years ago

@dilawar Thank you very much for your review and remarks. I have tried to rephrase the paragraph about LPJ-GUESS coupling in a clearer way. In the README, I mentioned that the educational version of LPJ-GUESS is not compatible with MMM.

Perhaps, the author would like to add expected results (plots) to the demo documentation.

I also thought about that. However, the example parameters and the plot script might change. After editing them, one could forget to update the screenshot of the expected demo output in the documentation. Then it can easily happen that the user’s output is different than the one in the docs, and the user might try to find an error where there is none. I didn’t come up with a good way to automate that, so I added a reference to the CI output.

dilawar commented 2 years ago

Thank you, @wtraylor.

@diehlpk I don't think I have any other issue.

diehlpk commented 2 years ago

Thank you, @wtraylor.

@diehlpk I don't think I have any other issue.

Thanks again for your review!

diehlpk commented 2 years ago

@wtraylor I will do the editorial comments by Monday and we can finish the paper next week.

diehlpk commented 2 years ago

@wtraylor I found some time and read your paper. I can recommend it for acceptance if you add this last change.

[ ] Through the instruction file, users can... I think it might be helpful to put a link (https://github.com/wtraylor/modular_megafauna_model/tree/master/examples) to the examples here. Or maybe add to the end of this paragraph: Example input files can be found here or whatever you prefer.

diehlpk commented 2 years ago

@dirmeier Can you please confirm that you are done with your review? Just want to make sure.

dirmeier commented 2 years ago

I conform we are finished here. Great work!

wtraylor commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago

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

whedon commented 2 years ago

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

wtraylor commented 2 years ago

@diehlpk I have added a footnote pointing to the example instruction files in the code.

I am currently debugging the CI for the documentation so I can create a release afterwards. I guess it makes sense to have the version that’s published in JOSS identifiable with a release tag.

diehlpk commented 2 years ago

@wtraylor Yes, please make a new version which has to include all the changes, you made during the JOSS review.

Please do the following

[ ] Post the new version number here.
[ ] Upload this version to Zenodo or FigShare and post the corresponding DOI here. Note that the title and the authors have to match with the PDF.

diehlpk commented 2 years ago

@wtraylor Any news on that? I would like to finish this paper soon and make room for a new submission.

wtraylor commented 2 years ago

@diehlpk I was able to fix the CI and released version 1.1.3 containing all changes from this review. It’s archived on Zenodo: 10.5281/zenodo.5779267

diehlpk commented 2 years ago

@whedon commands

whedon commented 2 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

diehlpk commented 2 years ago

@whedon set v1.1.3 as version

whedon commented 2 years ago

OK. v1.1.3 is the version.

diehlpk commented 2 years ago

@whedon set 10.5281/zenodo.5779267 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5779267 is the archive.

diehlpk commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago

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

whedon commented 2 years ago

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

diehlpk commented 2 years ago

@wtraylor The paper title

MMM: A C++ library for simulating large herbivores

does not match the title of the Zenodo archive

Modular Megafauna Model

Please change that, so I can accept the paper.

wtraylor commented 2 years ago

Please change that, so I can accept the paper.

I changed the title in the metadata of the Zenodo record (10.5281/zenodo.5779267).

diehlpk commented 2 years ago

@whedon set 10.5281/zenodo.5779267 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5779267 is the archive.

diehlpk commented 2 years ago

@whedon recommend-accept from branch joss-paper

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1016/j.rama.2018.06.006 is OK
- 10.1002/2016MS000904 is OK
- 10.2307/j.ctv1dwq0tq.9 is OK
- 10.1126/science.1251817 is OK
- 10.1034/j.1600-0706.2000.890209.x is OK
- 10.1016/j.ecolmodel.2013.04.025 is OK
- 10.1046/j.1466-822X.2001.t01-1-00256.x is OK
- 10.5194/bg-11-2027-2014 is OK
- 10.1038/s41559-018-0481-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 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/2826

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2826, 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-paper

diehlpk commented 2 years ago

@wtraylor Thanks, I recommend your paper to be accepted. One of the EIC will do a final check and publish the paper.

diehlpk commented 2 years ago

@dirmeier, @dilawar thank you so much for your reviews. We could not run JOSS without our reviwers.

kyleniemeyer commented 2 years ago

@whedon accept deposit=true from branch joss-paper

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 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/2828
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03631
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 2 years ago

Congratulations @wtraylor on your article's publication in JOSS!

Many thanks to @dirmeier and @dilawar for reviewing this, and @diehlpk for editing.

whedon commented 2 years ago

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.03631/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03631/status.svg
   :target: https://doi.org/10.21105/joss.03631

This is how it will look in your documentation:

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