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[REVIEW]: MimiBRICK.jl: A Julia package for the BRICK model for sea-level change in the Mimi integrated modeling framework
Submitting author: @tonyewong (Anthony Wong) Repository: https://github.com/raddleverse/MimiBRICK.jl Branch with paper.md (empty if default branch): Version: v1.0 Editor: @jbytecode Reviewers: @Zitzeronion, @svchb Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/0e0a2b8b9428ccf46394047ac801db61"><img src="https://joss.theoj.org/papers/0e0a2b8b9428ccf46394047ac801db61/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/0e0a2b8b9428ccf46394047ac801db61)
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
@tpoisot & @Zitzeronion, 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 @jbytecode 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
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.05 s (1039.7 files/s, 182034.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Julia 30 963 1580 2329
TOML 4 255 1 1184
Markdown 4 189 0 789
YAML 6 12 4 148
TeX 1 8 0 94
Jupyter Notebook 3 0 775 73
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SUM: 48 1427 2360 4617
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s10584-014-1080-9 is OK
- 10.1038/s41598-019-47587-6 is OK
- 10.1029/2018EF001082 is OK
- 10.5194/gmd-10-2495-2017 is OK
- 10.1073/pnas.1500515113 is OK
- 10.1002/2017EF000663 is OK
- 10.5194/gmd-10-2741-2017 is OK
- 10.17226/24651 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear reviewers @tpoisot and @Zitzeronion,
This is the review thread. Please type
@editorialbot generate my checklist
to generate your task list. In this list, there are 20 review items. Whenever you complete a task, you can check off the corresponding check box.
You can always interact with the author(s), other reviewers, and the editor during the reviewing process. You can also open issues in the target repo and send pull request. Please mention the review page in those issues, so we can keep tracking outside of our world.
Thank you in advance.
Review checklist for @Zitzeronion
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/raddleverse/MimiBRICK.jl?
- [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 (@tonyewong) 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, 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?
Hey @jbytecode,
I am sorry for the delay, started yesterday reviewing the project. So far so good, one thing that is somewhat conflicting to me is the Contribution and authorship. To my understanding, @lrennels (Lisa Rennels) is the creator and main contributor of the project. @tonyewong contributed, but it is hard for me to assess his commits as major contributions. Can @tonyewong please clarify this?
Thank you @Zitzeronion for stressing this point.
- It seems the initial state of the model is published elsewhere: Journal Article
- The first author is @tonyewong but they stated that the authors contributed equally to this work
- The abstract states that the initial attempts are written in R and FORTRAN.
- Does the role of @lrennels here consist of translating the original one into Julia? Why isn't @lrennels submitting autor?
- @tonyewong please clarify the issues that @Zitzeronion states.
Addition to this, the package is not installable using the standard way of Julia, e.g., Pkg> add package. Although it is not a rigid requirement, as JOSS editors, we always encourage the authors to register their packages into the proper package server.
@Zitzeronion @jbytecode 's assessment is accurate. I'm responsible for actively guiding/managing the project and doing some of the code development in tandem with @lrennels, who as you note is most active as a developer in terms of numbers of lines of code and commits.
Our team's understanding from the JOSS submission guidelines is that "active project direction" constitutes coauthor-worthy contributions to the project, and that the submitting author "must be a major contributor to the software" (emphasis added). But we did not see a rule that the submitting/first author must be the one who has written the most lines of code for this repository, or specific guidelines about how active project management/direction should be evaluated vs. lines of code or numbers of commits. If there is a requirement, please let us know and we will happily adjust the authorship. If not, all coauthors have agreed to the coauthor ordering and roles.
We will add the MimiBRICK.jl package to the general package registry. @davidanthoff I think you had started to do this - can you check into adding the package?
Thanks @jbytecode for putting such a nice bullet point list in such a short time. Thanks @tonyewong for the answer, maybe one additional question is @lrennels a PhD student under your supervision?
But we did not see a rule that the submitting/first author must be the one who has written the most lines of code for this repository, or specific guidelines about how active project management/direction should be evaluated vs. lines of code or numbers of commits.
I understand this reasoning, and I understand @tonyewong's role as active guiding/managing of the project. My only concern is that this statement can't be easily seen from the repositories' metadata.
At the end of the day, the repository owner is in the authors list and it seems @tonyewong has the full-control over the subject, software, and the other stuff, so that is okay for me. Of course, reviewers thoughts have higher priority in this stage to make a decision.
Thanks for the clarification!
@Zitzeronion , would a suitable solution be to add a section to the repository README.md file that outlines Author Contributions? Or perhaps more broadly a "Contributions" section where we can give credit to our various users/contributors?
Hello @tonyewong,
Yes, I would be satisfied with a short outline of contributions in the README.md file. I don't know if JOSS allows for an Authors contribution section, maybe @jbytecode knows?
The review threads are always attached to the published papers, so what we discussed here is available for those who are interested in.
We can leave this issue as is, or, of course it can be added as a small note in the paper as well as in the README.md.
I just submitted the package to the General Julia registry, see https://github.com/JuliaRegistries/General/pull/64547. It should get merged in about three days, which is currently the wait time for new package registrations.
@Zitzeronion @jbytecode I went ahead and added a brief Author Contributions section to the top-level README.md.
https://github.com/raddleverse/MimiBRICK.jl/pull/54#issue-1309801567
:wave: @tpoisot, please update us on how your review is going (this is an automated reminder).
:wave: @Zitzeronion, please update us on how your review is going (this is an automated reminder).
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1007/s10584-014-1080-9 is OK
- 10.1038/s41598-019-47587-6 is OK
- 10.1029/2018EF001082 is OK
- 10.5194/gmd-10-2495-2017 is OK
- 10.1073/pnas.1500515113 is OK
- 10.1002/2017EF000663 is OK
- 10.5194/gmd-10-2741-2017 is OK
- 10.17226/24651 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I've been active in the repo. There is just one thing left from the checkbox for the paper, which is State of the field.
The paper is well written, but I've hoped to see at least one comparison with another OSS package.
To keep @jbytecode updated - The comparison was added to the paper, and @Zitzeronion has closed the issue (https://github.com/raddleverse/MimiBRICK.jl/issues/52). Thanks for the useful feedback @Zitzeronion !