xnemogcm

[rcaneill]

as discussed in #154 I make a full submission

Submitting Author: Romain Caneill (@rcaneill)
All current maintainers: (@rcaneill)
Package Name: xnemogcm
One-Line Description of Package: Interface to open NEMO global circulation model output dataset with xarray and create a xgcm grid.
Repository Link: https://github.com/rcaneill/xnemogcm/
Version submitted: 0.4.2
Editor: @ocefpaf
Reviewer 1: @paigem
Reviewer 2: @callumrollo
Archive:
Version accepted: 0.4.3
JOSS DOI: N/A
Date accepted (month/day/year): 04/02/2024

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Description

xnemogcm is an interface to open NEMO ocean global circulation model output dataset and create a xgcm grid. NEMO 3.6, 4.0, and 4.2.0 are tested and supported. It can handle large simulations, is aware of meshgrid files, and makes it easy to handle the netCDF outputs od NEMO.

Scope

• Please indicate which category or categories.
  Check out our package scope page to learn more about our
  scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
  • Data validation and testing
  • Data visualization[^1]
  • Workflow automation
  • Citation management and bibliometrics
  • Scientific software wrappers
  • Database interoperability

Domain Specific & Community Partnerships

- [ ] Geospatial
- [ ] Education
- [x] Pangeo

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xnemogcm extracts the NEMO output and adds metadata (+ do some other things as change coordinate names, etc), and produces new xarray datasets. It is thus data processing.

• Who is the target audience and what are scientific applications of this package?

The target audience is anyone working with NEMO outputs and python. The scientific applications are any analyse that one want to do with NEMO outputs.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

Yes, xorca. My package differs as 1) it is more recent, updated to work with newer versions of NEMO, and 2) it uses a very different method to sort variables on the proper grid point (center, face, etc) (cf https://xgcm.readthedocs.io/en/latest/grids.html). xorca uses hardcoded variables, while xnemogcm uses attributes (either output directly by NEMO, or they can also be given while calling the processing functions).

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I made a pre-submission enquiry, issue #154

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[ocefpaf]

Editor in Chief checks

Hi there! Thank you for submitting your package for pyOpenSci
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Please check our Python packaging guide for more information on the elements
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Editor comments

[rcaneill]

Hi @ocefpaf,
thanks for taking care of this review :)

I can directly mention that some requirements are not fulfilled:

• API documentation: not done
• CONTRIBUTING.md: not done
• CODE_OF_CONDUCT.md: not done
• Issue Submission Documentation: not done

As far as I can say, the other requirements should be fulfilled.

[ocefpaf]

That's awesome! Here are a few minor comments/questions I have after the first pass:

• You mentioned that the GH repo is a mirror of a Gitlab one. IMO this dual repo usually leads to abandoned PRs in one place and/or stale code somewhere. Let alone the confusion to those finding the Software via search engines. I'm not against this setup and sometimes there are strong reasons to do so. However, if that can be avoided, it usually provides a smoother experience to all.
• Are you publishing the docs somewhere? I could not find them. I understand that the API docs are not ready but you do have some examples that can be the first form of user facing docs.
• I started checking the boxes above. Please let me know if I missed one that is already done.

[rcaneill]

That's awesome! Here are a few minor comments/questions I have after the first pass:

• You mentioned that the GH repo is a mirror of a Gitlab one. IMO this dual repo usually leads to abandoned PRs in one place and/or stale code somewhere. Let alone the confusion to those finding the Software via search engines. I'm not against this setup and sometimes there are strong reasons to do so. However, if that can be avoided, it usually provides a smoother experience to all.

Maybe the README is not so clear, the github is mirrored to gitlab (not from gitlab). The reason is that I do not want to force anyone to use github. But I could remove the sentence and keep my email address only.

• Are you publishing the docs somewhere? I could not find them. I understand that the API docs are not ready but you do have some examples that can be the first form of user facing docs.

No, I did not publish the doc anywhere. I started all the readthedoc machinery, but realised that having only these few examples was sufficient. As this packages has been developed only by me, I also had a lot to learn and a proper website for the doc was not urgent.

I can work on a proper website for the doc during this review process. I do not aim to change the content of the examples (unless I get comments from the reviewers), so I think the review can start without this implemented yet.

• I started checking the boxes above. Please let me know if I missed one that is already done.

[ocefpaf]

Maybe the README is not so clear, the github is mirrored to gitlab (not from gitlab). The reason is that I do not want to force anyone to use github. But I could remove the sentence and keep my email address only.

I understand. By making a choice we always end up making some folks unhappy. In my experience, mirroring like that always brings headaches in the long run. With that said, this is not important for your application here and you don't need to change that for PyOS.

I can work on a proper website for the doc during this review process. I do not aim to change the content of the examples (unless I get comments from the reviewers), so I think the review can start without this implemented yet.

@rcaneill we usually only start the review after all those points are checked. The reason is b/c the reviewers will read those docs and give you some feedback. Let me know if you need help setting docs, examples, etc in your repo. Once we are done I'll find two reviewers for your project and start the review process.

[rcaneill]

@rcaneill we usually only start the review after all those points are checked. The reason is b/c the reviewers will read those docs and give you some feedback. Let me know if you need help setting docs, examples, etc in your repo. Once we are done I'll find two reviewers for your project and start the review process.

Ok I understand, I will try to check all boxes in the following weeks!

[rcaneill]

Hi @ocefpaf , I updated the xnemogcm github repository, everything should be checked now! :D

[ocefpaf]

@rcaneill there seems to be a documentation build problem in page https://xnemogcm.readthedocs.io/en/latest/examples/recombing_mesh_mask_domain_cfg/

Also, some of your syntax there is not Windows friendly and users that copy-n-paste may find themselves with errors. Those are not blockers for us to continue but I wanted to give that feedback here before I forget.

We are now looking for 2 reviewers to start the process. Thank you!

[rcaneill]

@rcaneill there seems to be a documentation build problem in page https://xnemogcm.readthedocs.io/en/latest/examples/recombing_mesh_mask_domain_cfg/

thanks for catching this, it is now corrected.

Also, some of your syntax there is not Windows friendly and users that copy-n-paste may find themselves with errors. Those are not blockers for us to continue but I wanted to give that feedback here before I forget.

Are you speaking about the ls commands in the notebooks? If yes, I can change and use python instead.

[ocefpaf]

Are you speaking about the ls commands in the notebooks? If yes, I can change and use python instead.

That and I believe some of the paths may not be parsed correctly. I don't have a Windows machine to test in Path is smart enough to convert / to \ for us.

[rcaneill]

pathlib.Path is handling the windows conversion: https://stackoverflow.com/questions/2953834/how-should-i-write-a-windows-path-in-a-python-string-literal/68234511#68234511

For the ls, I changed to os.listdir in rcaneill/xnemogcm#80

[ocefpaf]

👋 Hi Callum Rollo and
Paige Martin!
Thank you for volunteering to review for pyOpenSci!

The following resources will help you complete your review:

1. Here is the reviewers guide. This guide contains all of the steps and information needed to complete your review.
2. Here is the review template that you will need to fill out and submit
   here as a comment, once your review is complete.

Please get in touch with any questions or concerns! Your review is due: March 5th, 2024 (3 weeks).
Please let us know if you need more time.

---

Reviewers: @callumrollo and @paigem
Due date: 2024-02-29

PS: You can comment, open issue, and/or PR directly in the xnemogcm for this review. Just make sure to cross-reference them here.

[callumrollo]

Hej Romain, I'm starting my review today. The package looks really good!

I see you have an Issue in to rename master >> main. Perhaps now is a good time to do that before I queue up a couple of small PRs rcaneill/xnemogcm#72

[callumrollo]

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

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The package includes all the following forms of documentation:

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For packages also submitting to JOSS

• The package has an obvious research application according to JOSS's definition in their submission requirements.

Note: Be sure to check this carefully, as JOSS's submission requirements and scope differ from pyOpenSci's in terms of what types of packages are accepted.

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Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing:

5 hours

---

Review Comments

• missing some badges from the README. PR ready Add badges to README rcaneill/xnemogcm#85
• missing installation instructions from README. PR ready Add installation instruction to README rcaneill/xnemogcm#86
• code does not currently meet PEP8. PR In progress add precommit rcaneill/xnemogcm#84
• contact emails inconsistent between readme and pyproject.toml outdated contact in pyproject.toml rcaneill/xnemogcm#81
• Missing docstring missing docstring rcaneill/xnemogcm#89

[rcaneill]

Hej Romain, I'm starting my review today. The package looks really good!

I see you have an Issue in to rename master >> main. Perhaps now is a good time to do that before I queue up a couple of small PRs rcaneill/xnemogcm#72

Hi Calum, thanks for your time :), I updated the name of the default branch to main

[rcaneill]

Thanks @callumrollo for all the PR and improvements.

@ocefpaf am I supposed to check / merge the PR on the fly, or wait for the end of the review?

[ocefpaf]

@ocefpaf am I supposed to check / merge the PR on the fly, or wait for the end of the review?

Up to you. Sometimes the second reviewer can add upon the first one and waiting makes sense. Sometimes merging/solving everything now makes it easier b/c it reduces the context for the second review.

[rcaneill]

Ok I'll try to merge on the way then

[callumrollo]

I've just about completed my review of the package. It looks to be in good shape! I particularly appreciate the comprehensive test suite. I've just raised one last issue with a missing docstring.

I don't work with nemo data, but using the example data provided I have tested that the functions in xnemogcm work as described. Hopefully @paigem can comment with some more domain specific expertise.

[rcaneill]

Thanks @callumrollo for you time and comments, I really appreciate.

[callumrollo]

If this package isn't being submitted to JOSS I believe my review is complete. Thanks @rcaneill for the speedy response to Issues and PRs

[paigem]

Thanks for your quick updates @rcaneill - it all looks great!

I'm continuing to go through my review checklist and have a couple questions:

• I commented in Add context in documentation around how this package fits in with existing packages rcaneill/xnemogcm#94 that this background information would be helpful to include in the README.
• Do you include citation information somewhere? I don't see it anywhere at the moment, but I may have missed it. PyOpenSci suggests adding it to your README.

I am continuing through the checklist and will reach out with any further questions.

[rcaneill]

I added CITATION.cff file in rcaneill/xnemogcm#104

[paigem]

@rcaneill I have finished my review! Thanks so much for your quick responses and for being so willing to accept feedback.

@ocefpaf This is to let you know that I have finished my review! Thanks for the opportunity, and let me know if there is anything else I've missed!

[rcaneill]

Thanks @paigem for your time, and for your great suggestions! I really appreciate.

[ocefpaf]

@rcaneill please let me know when you are done parsing the suggestions and please both reviewers for their +1 so we can move this application forward.

[rcaneill]

@ocefpaf I implemented / merged / commented all of their suggestions. So for me, we can move forward :)

[ocefpaf]

@ocefpaf I implemented / merged / commented all of their suggestions. So for me, we can move forward :)

Awesome! @paigem and @callumrollo can I get your +1 before we move to the next stage?

[callumrollo]

@ocefpaf lgtm!

[paigem]

Yes, everything looks great from my end! 😊

[ocefpaf]

@rcaneill I'm moving tomorrow and will be offline for a few days. I'll wrap this one up as soon as I get settle in our new place. If you don't hear from in ~1 week, please ping me again!

[ocefpaf]

---

🎉 xnemogcm has been approved by pyOpenSci! Thank you Romain Caneill (@rcaneill) for submitting xnemogcm and many thanks to Paige Martin (@paigem) and Callum Rollo (@callumrollo) for reviewing this package! 😸

Author Wrap Up Tasks

There are a few things left to do to wrap up this submission:

• Activate Zenodo watching the repo if you haven't already done so.
• Tag and create a release to create a Zenodo version and DOI.
• Add the badge for pyOpenSci peer-review to the README.md of xnemogcm. The badge should be [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/issue-number).
• Please fill out the post-review survey. All maintainers and reviewers should fill this out.

Editor Final Checks

Please complete the final steps to wrap up this review. Editor, please do the following:

• Make sure that the maintainers filled out the post-review survey
• Invite the maintainers to submit a blog post highlighting their package.
• Change the status tag of the issue to 6/pyOS-approved6 🚀🚀🚀.
• Invite the package maintainer(s) and both reviewers to slack if they wish to join.
• If the author submits to JOSS, please continue to update the labels for JOSS on this issue until the author is accepted (do not remove the 6/pyOS-approved label). Once accepted add the label 9/joss-approved to the issue. Skip this check if the package is not submitted to JOSS.

---

If you have any feedback for us about the review process please feel free to share it here. We are always looking to improve our process and documentation in the peer-review-guide.

[ocefpaf]

@rcaneill do you need help finalizing the 4 items in #155 (comment)?

Also, if you have some free time can you fill out our maintainers survey at https://forms.gle/BLGVCfUdiJHS5YJY7?
@paigem and @callumrollo same for you 😬 . Filling that form will help us improve the process.

[ocefpaf]

BTW, @rcaneill ! We want to invite you and your maintainer team to write a blog post (totally optional) on your package for us to promote your work! if you are interested - here are a few examples of other blog posts:

pandera
movingpandas

and here is a markdown example that you could use as a guide when creating your post.

it can even be a tutorial like post that highlights what your package does. then we can share it with people to get the word out about your package.

If you are too busy for this no worries. But if you have time - we'd love to spread the word about your package!

[ocefpaf]

Last but not least, do you (@rcaneill, @paigem, and @callumrollo) would like to be invited to PyOS slack? It will help you share your experience, get in touch with the community, and learn from others.

[rcaneill]

Hi @ocefpaf , I am on parental leave until Monday, I'll take time next week to answer you in details.

[ocefpaf]

Hi @ocefpaf , I am on parental leave until Monday, I'll take time next week to answer you in details.

Enjoy! I'm on forced* parental leave too so that is convenient for both of us 😄

(*Waiting for our day care application to be accepted so we can get the little one in school at the new home.)

[callumrollo]

Last but not least, do you (@rcaneill, @paigem, and @callumrollo) would like to be invited to PyOS slack? It will help you share your experience, get in touch with the community, and learn from others.

sure!

[rcaneill]

• Activate Zenodo watching the repo if you haven't already done so.
• Tag and create a release to create a Zenodo version and DOI.
• Add the badge for pyOpenSci peer-review to the README.md of xnemogcm. The badge should be .
• Please fill out the post-review survey. All maintainers and reviewers should fill this out.

The new xnemogcm version is 0.4.3, the doi is: https://doi.org/10.5281/zenodo.10973846

Thanks again @ocefpaf , @callumrollo, and @paigem for the review

[rcaneill]

Last but not least, do you (@rcaneill, @paigem, and @callumrollo) would like to be invited to PyOS slack? It will help you share your experience, get in touch with the community, and learn from others.

Thanks for the invite, but I prefer to not use Slack. I am still available by email for future exchanges.

[rcaneill]

BTW, @rcaneill ! We want to invite you and your maintainer team to write a blog post (totally optional) on your package for us to promote your work! if you are interested - here are a few examples of other blog posts:

pandera movingpandas

and here is a markdown example that you could use as a guide when creating your post.

it can even be a tutorial like post that highlights what your package does. then we can share it with people to get the word out about your package.

If you are too busy for this no worries. But if you have time - we'd love to spread the word about your package!

I will see if I have time for it. If so, should I open a PR on https://github.com/pyOpenSci/pyopensci.github.io?

[ocefpaf]

I will see if I have time for it. If so, should I open a PR on https://github.com/pyOpenSci/pyopensci.github.io?

Yes. You can see an example here.

[ocefpaf]

I'm closing this as complete. Thanks again for the reviewers and for @rcaneill for your patience!