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[REVIEW]: cgeniepy: A Python package for analysing cGENIE Earth System Model output #6762

Closed editorialbot closed 2 months ago

editorialbot commented 6 months ago

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

Status

status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b08301b8ec79f1da9150cec224da8391/status.svg)](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

πŸ“ Checklist for @koldunovn

πŸ“ Checklist for @jimmielin

editorialbot commented 6 months ago

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 6 months ago
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
editorialbot commented 6 months ago

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
editorialbot commented 6 months ago

Paper file info:

πŸ“„ Wordcount for paper.md is 683

βœ… The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

🟑 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 6 months ago

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

rwegener2 commented 6 months ago

πŸ‘‹πŸΌ @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 commented 6 months ago

πŸ‘‹πŸΌ @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

koldunovn commented 6 months ago

Review checklist for @koldunovn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jimmielin commented 6 months ago

Review checklist for @jimmielin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rwegener2 commented 4 months ago

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!

jimmielin commented 4 months ago

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.

Otherwise it looks good and I'm happy to accept with minor revisions. Great work! Haipeng

koldunovn commented 4 months ago

@rwegener2 Will try to do evaluation this week, sorry for the delay.

rwegener2 commented 4 months ago

Thanks @koldunovn

rwegener2 commented 3 months ago

Hi @koldunovn πŸ‘‹πŸ» Just checking in. Any updates on your end?

rwegener2 commented 3 months ago

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.

ruiying-ocean commented 3 months ago

@rwegener2 Thanks Rachel, good to know this because I've been waiting for the other comment. I'll revise the manuscript soon.

ruiying-ocean commented 3 months ago

Hi @jimmielin,

Thanks for your appreciation and useful comments!

For your questions,

  1. The 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)
  2. 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

koldunovn commented 2 months ago

Review checklist for @koldunovn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

koldunovn commented 2 months ago

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.

rwegener2 commented 2 months ago

Thanks for the update @koldunovn!

@jimmielin were your feedback appropriately addressed in @ruiying-ocean's last comment?

ruiying-ocean commented 2 months ago

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!

koldunovn commented 2 months ago

Looks goos, no questions from my side anymore.

ruiying-ocean commented 2 months ago

@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.

rwegener2 commented 2 months ago

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?

rwegener2 commented 2 months ago

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.

ruiying-ocean commented 2 months ago

@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.

jimmielin commented 2 months ago

Looks good to me, thank you! Congratulations.

rwegener2 commented 2 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Editor checks paper proof:

Editor checks archive generated by author:

Editor double checks paper and recommends submission:

rwegener2 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

rwegener2 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

βœ… 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

🟑 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,...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
rwegener2 commented 2 months ago

@ruiying-ocean at this point could you please:

In the meantime I will review the manuscript. Thanks!

ruiying-ocean commented 2 months ago

@rwegener2

Let me know if anything is needed, thank you!

rwegener2 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

rwegener2 commented 2 months ago

Hi @ruiying-ocean πŸ‘‹πŸ» 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.

ruiying-ocean commented 2 months ago

@rwegener2 Thank you Rachel! I have revised the paper according to your comments. Please do let me know anywhere to improve.

rwegener2 commented 2 months ago

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 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

rwegener2 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

βœ… 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

🟑 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
ruiying-ocean commented 2 months ago

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

rwegener2 commented 2 months ago

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?

rwegener2 commented 2 months ago

@editorialbot set v0.14.2 as version

editorialbot commented 2 months ago

Done! version is now v0.14.2

rwegener2 commented 2 months ago

@editorialbot set https://zenodo.org/records/13835532 as archive

editorialbot commented 2 months ago

That doesn't look like a valid DOI value