Closed editorialbot closed 2 months ago
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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:
π Wordcount for paper.md
is 683
β
The paper includes a Statement of need
section
License info:
π‘ License found: GNU General Public License v3.0
(Check here for OSI approval)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
ππΌ @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.
ππΌ @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.
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
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.
Interpolator
class - could you clarify what it is used for and if you used any packages for this?Otherwise it looks good and I'm happy to accept with minor revisions. Great work! Haipeng
@rwegener2 Will try to do evaluation this week, sorry for the delay.
Thanks @koldunovn
Hi @koldunovn ππ» Just checking in. Any updates on your end?
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,
Interpolator
class is based on scipy.interpolate
and 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)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
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!
Looks goos, no questions from my side anymore.
@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.
Looks good to me, thank you! Congratulations.
Editor checks paper proof:
@editorialbot generate pdf
), check all references have DOIs, follow the links and check the references (@editorialbot check references
)Editor checks archive generated by author:
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
Editor double checks paper and recommends submission:
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
β
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
- 10.1002/2013PA002552 is OK
π‘ SKIP 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,...
β MISSING DOIs
- None
β INVALID DOIs
- None
@ruiying-ocean at this point could you please:
In the meantime I will review the manuscript. Thanks!
@rwegener2
Let me know if anything is needed, thank you!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @ruiying-ocean ππ» I read through the manuscript. It looks good! I just made a few small changes and comments on confusing lines in https://github.com/ruiying-ocean/cgeniepy/pull/7. Let me know if you have anything isn't clear.
@rwegener2 Thank you Rachel! I have revised the paper according to your comments. Please do let me know anywhere to improve.
Great. Thanks @ruiying-ocean!
Would you please create an updated DOI/version tag for the submission? (I apologize I should have waited to ask you to do this the first time until after my review). You should be able to upload a new version to the same zenodo artifact and not need to create a whole new submission.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
β
OK DOIs
- 10/ggbnrm is OK
- 10.1038/s41586-022-05018-z is OK
- 10.5281/zenodo.5724577 is OK
- 10.5281/zenodo.13766391 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
- 10.1002/2013PA002552 is OK
π‘ SKIP DOIs
- None
β MISSING DOIs
- None
β INVALID DOIs
- None
Great. Thanks @ruiying-ocean!
Would you please create an updated DOI/version tag for the submission? (I apologize I should have waited to ask you to do this the first time until after my review). You should be able to upload a new version to the same zenodo artifact and not need to create a whole new submission.
@rwegener2 Yes! I have published a new release and it will appear soon in the same zenodo record
I have published a new release and it will appear soon in the same zenodo record
Thanks @ruiying-ocean! So the correct version tag is now v0.14.2, correct? And the DOI is https://doi.org/10.5281/zenodo.13835532?
@editorialbot set v0.14.2 as version
Done! version is now v0.14.2
@editorialbot set https://zenodo.org/records/13835532 as archive
That doesn't look like a valid DOI value
Submitting author: !--author-handle-->@ruiying-ocean<!--end-author-handle-- (Rui Ying) Repository: https://github.com/ruiying-ocean/cgeniepy Branch with paper.md (empty if default branch): master Version: v0.14.2 Editor: !--editor-->@rwegener2<!--end-editor-- Reviewers: @koldunovn, @jimmielin Archive: 10.5281/zenodo.13835532
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@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:
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