[REVIEW]: MetaCast: A package for broadCASTing epidemiological and ecological models over META-populations.

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@m-d-grunnill@mstimberg<!--end-editor-- Reviewers: @acolum, @robmoss Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d/status.svg)](https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d)

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

@acolum & @robmoss, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mstimberg 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 ✨

Checklists

📝 Checklist for @acolum

📝 Checklist for @robmoss

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

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

OK DOIs

- 10.2307/j.ctvcm4gk0.10 is OK
- 10.18637/jss.v098.i10 is OK
- 10.48550/arXiv.1803.06934 is OK
- 10.1371/JOURNAL.PCBI.1011018 is OK
- 10.18637/jss.v094.i06 is OK
- 10.1371/journal.pcbi.1009149 is OK
- 10.21105/joss.03097 is OK
- 10.18637/jss.v104.i04 is OK
- 10.18637/jss.v084.i08 is OK
- 10.21105/joss.03539 is OK
- 10.21105/joss.03247 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (891.8 files/s, 195560.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            405           1270           1762
XML                              7              0              0            694
Jupyter Notebook                 1              0           2299            413
Markdown                         4            108              0            352
TeX                              1              2              0            179
TOML                             1              4              2             58
YAML                             2              7             17             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
reStructuredText                 1              5              8              7
-------------------------------------------------------------------------------
SUM:                            35            543           3604           3528
-------------------------------------------------------------------------------

Commit count by author:

    65  Martin Grunnill

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 990

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 1 month ago

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

mstimberg commented 1 month ago

👋🏼 @m-d-grunnill, @acolum, and @robmoss – this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

There are additional guidelines in the message at the start of this issue.

Please feel free to ping me (@mstimberg) if you have any questions/concerns.

acolum commented 1 month ago

Review checklist for @acolum

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 https://github.com/m-d-grunnill/MetaCast?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@m-d-grunnill) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[x] 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)?
[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?

acolum commented 1 month ago

@mstimberg Thank you for setting up this review thread. I have a brief question regarding the JOSS Guidelines. Under the Substantial Scholarly Effort section, it is mentioned that: "As a rule of thumb, JOSS’ minimum allowable contribution should represent not less than three months of work for an individual." However, the package repository's commit history appears to be only ~2 months long (from February 6 - April 2, 2024). I was wondering if this suggests that the submission may not fully align with the aforementioned guidelines.

mstimberg commented 1 month ago

Hi @acolum, thanks for looking into this. If I am not mistaken (please don't hesitate to chime in @m-d-grunnill), the repository continues/builds on work that has been done in other repositories by the same authors (e.g. https://github.com/LIAM-COVID-19-Forecasting/Modelling-Disease-Mitigation-at-Mass-Gatherings-A-Case-Study-of-COVID-19-at-the-2022-FIFA-World-Cup). The comments on top of some source files (e.g. https://github.com/m-d-grunnill/MetaCast/blob/main/src/metacast/infection_seeding.py) also seem to indicate that development started in 2022, so I think the basic criteria for "substantial scholarly effort" are fulfilled. Please also note that the EiC submitted the publication to a "scope check" by the editorial board (mostly due to the potential conflict with the paper associated to the GitHub repository linked above), which agreed that the submission is in scope for JOSS.

acolum commented 1 month ago

@mstimberg Thank you very much for these clarifications. I'll resume my review.

m-d-grunnill commented 1 month ago

As described by @mstimberg the work builds on the code used in the publication. We put the code for that publication github for transparency. We made the code much more generalizable, added further quality of life changes and packaged the code up for pip. This newer version is what has been submitted to JOSS.

acolum commented 3 weeks ago

Thank you both!

Overall, everything looks great except for some issues in the paper, which I've outlined in this issue. Once these are resolved, I'd recommend accepting this submission.

robmoss commented 3 weeks ago

Review checklist for @robmoss

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 https://github.com/m-d-grunnill/MetaCast?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@m-d-grunnill) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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)?
[ ] 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, who the target audience is, and its relation to other work?
[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?

m-d-grunnill commented 3 weeks ago

This is the first time I have submitted a paper to JOSS. Should I be working on the corrections from the first reviewer, before the 2nd reviewer finishes. OR should I wait until the 2nd reviewer has given their corrections.

mstimberg commented 3 weeks ago

@m-d-grunnill there is no clear rule for this on JOSS. Usually, if you agree with the changes suggested by a reviewer, you can apply them right-away. The only situation where I'd strongly recommend waiting for feedback from the other reviewer is if a proposed change is very fundamental. Slightly rewriting the text, fixing grammar/spelling mistakes, etc. definitely do not need a sign-off from the other reviewer. Hope that clears things up, do not hesitate to ping me again if you have further questions.

robmoss commented 2 weeks ago

@m-d-grunnill my apologies for the delay in completing my review. I have several imminent contract deadlines that are taking up all of my available time, and I'm aiming to complete my review in the next 2 weeks. I don't think I'll make any suggestions that conflict with those of @acolum, so please feel free to address their suggestions whenever suits you. Sincerely, Rob

robmoss commented 1 week ago

@m-d-grunnill @mstimberg I've completed my review and filed several issues regarding:

Once these are resolved, I'm happy to recommend accepting this submission :)

m-d-grunnill commented 4 days ago

Thanks for the review @robmoss and @acolum. I am starting the corrections.

@mstimberg I have started the corrections to the paper.md file. @acolum points out "Under Acknowledgements and Funding, the bullet points are not rendering correctly in the PDF". This renders fine in normal md format. I am not sure how to fix this?

robmoss commented 4 days ago

@mstimberg I have started the corrections to the paper.md file. @acolum points out "Under Acknowledgements and Funding, the bullet points are not rendering correctly in the PDF". This renders fine in normal PDF. I am not sure how to fix this?

@m-d-grunnill I'm not entirely sure how to fix this, but perhaps try inserting a blank line between the preceding sentence ("The authors of this manuscript ...") and the first list item?

mstimberg commented 4 days ago

@m-d-grunnill I'm not entirely sure how to fix this, but perhaps try inserting a blank line between the preceding sentence ("The authors of this manuscript ...") and the first list item?

I agree that this is probably an issue of a missing blank line. Please try and let us know if that doesn't fix it.

m-d-grunnill commented 2 days ago

All the issues raised by the reviewers have been addressed and the issues are closed see:

Being my first submission to JOSS I am unsure of what the next steps are.

mstimberg commented 2 days ago

Thanks for the update @m-d-grunnill. @robmoss , @acolum, can you confirm that all your issues have been addressed and that you recommend acceptance of the manuscript/code in its current state? For completeness, please also check the remaining boxes in your checklist :pray:

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