joss-reviews
joss-reviews copied to clipboard
openjournals
[REVIEW]: cgeniepy: A Python package for analysing cGENIE Earth System Model output
Submitting author: @ruiying-ocean (Rui Ying) Repository: https://github.com/ruiying-ocean/cgeniepy Branch with paper.md (empty if default branch): master Version: 0.12.0 Editor: @rwegener2 Reviewers: @koldunovn, @jimmielin Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/b08301b8ec79f1da9150cec224da8391"><img src="https://joss.theoj.org/papers/b08301b8ec79f1da9150cec224da8391/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/b08301b8ec79f1da9150cec224da8391)
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
@koldunovn & @jimmielin, 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 @rwegener2 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
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10/ggbnrm is OK
- 10.1038/s41586-022-05018-z is OK
- 10/dcq62d is OK
- 10.5194/gmd-16-813-2023 is OK
- 10.31223/X5D10G is OK
- 10.1073/pnas.2205326119 is OK
- 10/gbtdts is OK
MISSING DOIs
- No DOI given, and none found for title: Interface to open NEMO ocean global circulation mo...
- No DOI given, and none found for title: Tools to interact with MITgcm (setup, run, output,...
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=0.12 s (794.1 files/s, 214524.8 lines/s)
--------------------------------------------------------------------------------
Language files blank comment code
--------------------------------------------------------------------------------
XML 2 48 258 8696
SVG 1 0 0 7466
Python 36 913 1055 2644
reStructuredText 28 1018 1150 229
Bourne Again Shell 1 37 112 219
SQL 1 0 18 144
TeX 1 8 0 136
Jupyter Notebook 16 0 860 112
Markdown 3 53 0 98
YAML 2 8 21 28
DOS Batch 1 8 1 26
make 1 4 7 9
TOML 1 1 0 8
--------------------------------------------------------------------------------
SUM: 94 2098 3482 19815
--------------------------------------------------------------------------------
Commit count by author:
311 Rui Ying (Mac)
45 ruiying-ocean
21 Rui Ying
Paper file info:
📄 Wordcount for paper.md is 683
✅ The paper includes a Statement of need section
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
👋🏼 @ruiying-ocean @koldunovn @jimmielin 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.
These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.
Please feel free to ping me (@rwegener2) if you have any questions/concerns.
👋🏼 @ruiying-ocean @koldunovn @jimmielin 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 checklistas the top of a new comment in this thread.
These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention
openjournals/joss-reviews#REVIEW_NUMBERso that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.
Please feel free to ping me (@rwegener2) if you have any questions/concerns.
Thank you Rachel! Also thank Nikolay and Haipeng for being my reviewers! Let me know anything that I can do or improve while you are checking those criterias
Review checklist for @koldunovn
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 https://github.com/ruiying-ocean/cgeniepy?
- [ ] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- [ ] Contribution and authorship: Has the submitting author (@ruiying-ocean) 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
- [ ] 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.
- [ ] 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
- [ ] 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: 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?
- [ ] 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 @jimmielin
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/ruiying-ocean/cgeniepy?
- [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 (@ruiying-ocean) 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?
- [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 @jimmielin and @koldunovn! Just checking in to see how your review is going. If you have any questions please don't hesitate to reach out!
Hi @ruiying-ocean and @rwegener2,
Apologies for the delay. The software and the description manuscript looks good. I just have a few questions regarding the implementation / package design that maybe could be clarified in the manuscript.
- You mention there is a
Interpolatorclass - could you clarify what it is used for and if you used any packages for this? - It would be useful to provide some examples of model-data comparison, whether your package can ingest observational data for comparisons, example of the skill score calculation, etc.
Otherwise it looks good and I'm happy to accept with minor revisions. Great work! Haipeng
Thanks @jimmielin for the comments! The JOSS review process is iterative, so @ruiying-ocean feel free to address those comments at anytime. @jimmielin will need an update before he can approve the review.
@rwegener2 Thanks Rachel, good to know this because I've been waiting for the other comment. I'll revise the manuscript soon.
Hi @jimmielin,
Thanks for your appreciation and useful comments!
For your questions,
- The
Interpolatorclass is based onscipy.interpolateand it is designed for increasing the grid resolution of cGENIE and creating prettier figure (e.g., the vertical distribution of nutrient, O2, https://cgeniepy.readthedocs.io/en/latest/auto_examples/plot_PO4_distribution.html#sphx-glr-auto-examples-plot-po4-distribution-py) - I have added a section for this according to your suggestion.
Both are incorporated in the updated manuscript, which can be found in the https://github.com/ruiying-ocean/cgeniepy/actions if you go to the latest sucessful build.
Hi @ruiying-ocean and @rwegener2,
Apologies for the delay. The software and the description manuscript looks good. I just have a few questions regarding the implementation / package design that maybe could be clarified in the manuscript.
* You mention there is a `Interpolator` class - could you clarify what it is used for and if you used any packages for this? * It would be useful to provide some examples of model-data comparison, whether your package can ingest observational data for comparisons, example of the skill score calculation, etc.Otherwise it looks good and I'm happy to accept with minor revisions. Great work! Haipeng
Review checklist for @koldunovn
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/ruiying-ocean/cgeniepy?
- [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 (@ruiying-ocean) 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?
- [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?
I have only one remaining issue on updating the examples ruiying-ocean/cgeniepy#1 As soon as it is addressed we are good to go.
Thanks for the update @koldunovn!
@jimmielin were your feedback appropriately addressed in @ruiying-ocean's last comment?
I have only one remaining issue on updating the examples ruiying-ocean/cgeniepy#1 As soon as it is addressed we are good to go.
The example scripts are updated to avoid hard codes. Please check them and I appreciate your help!
@rwegener2 Rachel do you know how long it takes to get a doi after this paper being accepted? I am now pre-proofing another paper and I am happy to update the reference if this is within 2 weeks.
Looks goos, no questions from my side anymore.
Thanks, @koldunovn! If you are satisfied with the submission would you please confirm by checking off the remaining boxes in your review checklist?
Rachel do you know how long it takes to get a doi after this paper being accepted? I am now pre-proofing another paper and I am happy to update the reference if this is within 2 weeks.
@ruiying-ocean After reviewers are satisfied with submission it usually takes 3-7 days to finalize the publication/get a DOI. After reviewers confirm approval I generate a final checklist that will include items for you and for myself. I'll ask you to upload your code to Zenodo (or similar) and generate a code DOI at that point. Once I you generate DOI and complete my checks the submission gets sent back to the Track Editor, who finalizes the paper publication and closes the issue. The paper will get a DOI when it is published.
@rwegener2 That is very detailed and helpful! Thanks, Rachel!
Rachel do you know how long it takes to get a doi after this paper being accepted? I am now pre-proofing another paper and I am happy to update the reference if this is within 2 weeks.
@ruiying-ocean After reviewers are satisfied with submission it usually takes 3-7 days to finalize the publication/get a DOI. After reviewers confirm approval I generate a final checklist that will include items for you and for myself. I'll ask you to upload your code to Zenodo (or similar) and generate a code DOI at that point. Once I you generate DOI and complete my checks the submission gets sent back to the Track Editor, who finalizes the paper publication and closes the issue. The paper will get a DOI when it is published.
Post-Review Checklist for Editor and Authors
Additional Author Tasks After Review is Complete
- Double check authors and affiliations (including ORCIDs)
- Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
- Archive the release on Zenodo/figshare/etc and post the DOI here.
- Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
- Make sure that the license listed for the archive is the same as the software license.
Editor Tasks Prior to Acceptance
Editor checks paper proof:
- [x] Download the proof (
@editorialbot generate pdf), check all references have DOIs, follow the links and check the references (@editorialbot check references) - [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
Editor checks archive generated by author:
- [x] Check that the archive title ✅, author list ✅, version tag ✅, and the license ✅ are correct
- [x] Set archive DOI with
@editorialbot set <DOI here> as archive - [x] Set version with
@editorialbot set <version here> as version
Editor double checks paper and recommends submission:
- [x] Double check rendering of paper with
@editorialbot generate pdf - [x] Specifically check the references with
@editorialbot check referencesand ask author(s) to update as needed - [x] Recommend acceptance with
@editorialbot recommend-accept