[REVIEW]: xCDAT: A Python package for simple climate data analysis on structured grids

[editorialbot]

Submitting author: @tomvothecoder (Tom Vo)
Repository: https://github.com/xCDAT/xcdat
Branch with paper.md (empty if default branch): main
Version: v0.7.1
Editor: @arfon
Reviewers: @brian-rose, @mgrover1
Archive: 10.5281/zenodo.12522560

Status

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Markdown: [![status](https://joss.theoj.org/papers/aeeaf960da55c95d4b0d6b690442578a/status.svg)](https://joss.theoj.org/papers/aeeaf960da55c95d4b0d6b690442578a)

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

@brian-rose & @mgrover1, 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 @arfon 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

📝 Checklist for @mgrover1

📝 Checklist for @brian-rose

[editorialbot]

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.24 s (318.5 files/s, 231422.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           2601           3711          11193
reStructuredText                17            663            324           1476
Jupyter Notebook                 9              0          34843            548
YAML                            12             52             45            454
TeX                              1             15              0            380
Markdown                         2             40              0             91
make                             2             21             16             65
TOML                             2             10             22             56
DOS Batch                        1              8              1             27
SVG                              6              0              1             20
-------------------------------------------------------------------------------
SUM:                            78           3410          38963          14310
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1637

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5194/gmd-10-4619-2017 is OK
- 10.5334/jors.148 is OK
- 10.5194/egusphere-2023-2720 is OK
- 10.1073/pnas.2209431119 is OK
- 10.1109/ICDMW.2009.64 is OK
- 10.1002/2014EO420002 is OK
- 10.5194/gmd-15-9031-2022 is OK
- 10.5281/zenodo.2586088 is OK
- 10.5281/zenodo.10038784 is OK
- 10.5281/zenodo.8339034 is OK
- 10.5281/zenodo.10236521 is OK
- 10.5281/zenodo.8356796 is OK
- 10.5281/zenodo.7348619 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1029/2022MS003156 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[arfon]

@tomvothecoder, @brian-rose, @mgrover1 – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also 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 https://github.com/openjournals/joss-reviews/issues/6426 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[arfon]

@brian-rose, @mgrover1 – I don't see any progress yet from either of you on your reviews. Is there anything I can do to help you get going here?

[mgrover1]

I am taking a look this week - thanks for the reminder @arfon

[mgrover1]

Review checklist for @mgrover1

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/xCDAT/xcdat?
• 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 (@tomvothecoder) 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?

[mgrover1]

@tomvothecoder - I went through with a first cut. I am struggling to reproduce the benchmarks you mention due to trying to run on an M1 machine, I plan to test with my intel Mac later this week.

Most of the comments are tracked in the associated the issues. I recently added the DOI linking issue as well. Here is a list of the related issues to close:

• Bug: Unable to create conda environment for development environment on M1 Mac xCDAT/xcdat#619
• BUG: Unable to reproduce the "Calculating Climatology and Departures from Time Series Data" Example xCDAT/xcdat#620
• BUG: Incorrect DOI Reference in Paper Draft xCDAT/xcdat#621
• DOC: Add clarification that this only runs on non-M1 mac machines xCDAT/xcdat-validation#51

The writing is well done, and the documentation is fantastic - just a couple of environment issues that likely would be fixed with some additional CI/cross architecture tests.

[tomvothecoder]

@mgrover1 Thanks a lot for you review so far! I'm addressing those GitHub issues ASAP and will let you know once they are all resolved.

[tomvothecoder]

@mgrover1 All of the issues listed in your comment above should now be resolved!

[mgrover1]

Round 2 of reviews

Thanks for addressing all of the previous comments!

@tomvothecoder - is there anyway to make the datasets mentioned in the benchmarks more accessible? I understand one of the files is 105 GB, but I think it would help with reproducibility if there were someway to download these locally and execute the validation scripts you all put together.

• DOC: Include instructions on how to access the datasets used for benchmarks xCDAT/xcdat-validation#52

[tomvothecoder]

@tomvothecoder - is there anyway to make the datasets mentioned in the benchmarks more accessible? I understand one of the files is 105 GB, but I think it would help with reproducibility if there were someway to download these locally and execute the validation scripts you all put together.

@mgrover1 Good point! I'll check to see if those datasets are available on ESGF and Globus. I'll also update the instructions for running the performance benchmark script to make it easier to reproduce the results.

[mgrover1]

Great!! Thanks!!

[arfon]

@brian-rose – just checking in again here. We have one complete review from @mgrover1 at this point and would love to have yours completed in the next couple of weeks. What do you think?

[brian-rose]

Hi @arfon yes I will get this done soon. Thanks for the nudge!

[mgrover1]

The revised instructions work well - thanks @tomvothecoder for making those changes!

[tomvothecoder]

@mgrover1 Awesome, thanks Max!

[brian-rose]

I checked off the "Example usage" box, and I enthusiastically recommend this paper for publication in JOSS.

[tomvothecoder]

Hi @arfon, is anything else needed for the review of this paper?

[arfon]

@brian-rose – thanks for getting your review in 🙏

@tomvothecoder – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• I can then move forward with accepting the submission.

[tomvothecoder]

Hi @arfon, I completed your final checklist your comment above. Thanks!

• please give your own paper a final read to check for any potential typos etc. -- I only updated the date to 24 June 2024 here
• make a new release of this software that includes the changes that have resulted from this review (https://github.com/xCDAT/xcdat/releases/tag/v0.7.1)
• make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive (link)
  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors
• update this thread with the DOI of the archive: 10.5281/zenodo.12522560

[arfon]

@editorialbot set 10.5281/zenodo.12522560 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.12522560

[arfon]

@editorialbot set v0.7.1 as version

[editorialbot]

Done! version is now v0.7.1

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

⚠️ Error preparing paper acceptance.

[arfon]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1029/2022MS003156 is OK
- 10.5194/gmd-10-4619-2017 is OK
- 10.5334/jors.148 is OK
- 10.5194/egusphere-2023-2720 is OK
- 10.1073/pnas.2209431119 is OK
- 10.1109/ICDMW.2009.64 is OK
- 10.1002/2014EO420002 is OK
- 10.5194/gmd-15-9031-2022 is OK
- 10.5281/zenodo.2586088 is OK
- 10.5281/zenodo.10038784 is OK
- 10.5281/zenodo.8339034 is OK
- 10.5281/zenodo.10236521 is OK
- 10.5281/zenodo.8356796 is OK
- 10.5281/zenodo.7348619 is OK

MISSING DOIs

- No DOI given, and none found for title: Dask: Library for dynamic task scheduling
- No DOI given, and none found for title: E3SM-Unified: A metapackage for a unified anaconda...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5552, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Vo
  given-names: Tom
  orcid: "https://orcid.org/0000-0002-2461-0191"
- family-names: Po-Chedley
  given-names: Stephen
  orcid: "https://orcid.org/0000-0002-0390-238X"
- family-names: Boutte
  given-names: Jason
  orcid: "https://orcid.org/0009-0009-3996-3772"
- family-names: Lee
  given-names: Jiwoo
  orcid: "https://orcid.org/0000-0002-0016-7199"
- family-names: Zhang
  given-names: Chengzhu
  orcid: "https://orcid.org/0000-0002-9632-0716"
doi: 10.5281/zenodo.12522560
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Vo
    given-names: Tom
    orcid: "https://orcid.org/0000-0002-2461-0191"
  - family-names: Po-Chedley
    given-names: Stephen
    orcid: "https://orcid.org/0000-0002-0390-238X"
  - family-names: Boutte
    given-names: Jason
    orcid: "https://orcid.org/0009-0009-3996-3772"
  - family-names: Lee
    given-names: Jiwoo
    orcid: "https://orcid.org/0000-0002-0016-7199"
  - family-names: Zhang
    given-names: Chengzhu
    orcid: "https://orcid.org/0000-0002-9632-0716"
  date-published: 2024-06-29
  doi: 10.21105/joss.06426
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6426
  title: "xCDAT: A Python Package for Simple and Robust Analysis of
    Climate Data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06426"
  volume: 9
title: "xCDAT: A Python Package for Simple and Robust Analysis of
  Climate Data"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06426 joss-papers#5553
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06426
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@brian-rose, @mgrover1 – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@tomvothecoder – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.06426

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[tomvothecoder]

@brian-rose, @mgrover1 – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@tomvothecoder – your paper is now accepted and published in JOSS ⚡🚀💥

Thanks @arfon for facilitating the review process for this paper! I am grateful and excited to have this xCDAT paper published in JOSS. This is a great milestone for the project.

And big thanks to @brian-rose and @mgrover1 for your diligent review. I appreciate your time and interest in xCDAT! Feel free to reach out if you ever need anything xCDAT related (or a review of a paper like this) :)