[REVIEW]: ndbc-api: Accelerating oceanography and climate science research with Python

[editorialbot]

Submitting author: @CDJellen (Chris Jellen)
Repository: http://github.com/cdjellen/ndbc-api
Branch with paper.md (empty if default branch): user/cjellen/joss-paper-submission
Version: v0.24.12.02.1
Editor: @cheginit
Reviewers: @rwegener2, @ks905383
Archive: 10.5281/zenodo.14261355

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7650fcdcf5309f37067b9f271f12e438/status.svg)](https://joss.theoj.org/papers/7650fcdcf5309f37067b9f271f12e438)

Reviewers and authors:

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Reviewer instructions & questions

@rwegener2 & @ks905383, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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✨ 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 @ks905383

📝 Checklist for @rwegener2

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=1.34 s (134.6 files/s, 685439.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                            39         374062             43         504544
Python                         135           1337            518           4983
Markdown                         2             69              0            214
Jupyter Notebook                 1              0          30859             61
TeX                              1              3              0             31
TOML                             1              3              0             27
INI                              1              0              0              4
-------------------------------------------------------------------------------
SUM:                           180         375474          31420         509864
-------------------------------------------------------------------------------

Commit count by author:

    95	CDJellen
    41	cdjellen
    16	Chris Jellen
     1	abdu558

[editorialbot]

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

✅ OK DOIs

- 10.25080/majora-92bf1922-00a is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: NDBC Web Data Guide
- No DOI given, and none found for title: NDBC Active Stations
- No DOI given, and none found for title: NetCDF4 Python Library

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 600

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[cheginit]

👋🏼 @CDJellen, @rwegener2, and @ks905383, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step, as mentioned in the first comment of this issue, 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#7406 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 notify me 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 don't hesitate to ping me (@cheginit) if you have any questions/concerns.

[editorialbot]

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

[ks905383]

Review checklist for @ks905383

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 http://github.com/cdjellen/ndbc-api?
• 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 (@CDJellen) 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?

[rwegener2]

Review checklist for @rwegener2

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 http://github.com/cdjellen/ndbc-api?
• 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 (@CDJellen) 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?

[cheginit]

👋🏼 @rwegener2, @ks905383 a friendly reminder for this review.

[ks905383]

Thanks for the reminder - will look at this this week.

[ks905383]

@CDJellen Could you clarify something on the modes? The docs say that the different modes '[correspond] to the data formats provided by the NDBC data service'. I'm not quite sure how that maps onto the data. I see that some of the modes carry some of the same variables, but that the same timestamp + station can give different values for those variables (like WDIR, WSPD, and GST in the example above). Would a user more familiar with this dataset know the difference between those two rows, or should there be a flag / column (/ df index) specifying which data format each row came from?
(apologies, I haven't worked with this specific dataset before)

Thanks!

[CDJellen]

Thank you so much for your thorough review @ks905383; the "modes" that the API supports map directly to the data modalities outlined in the web data guide. While I believe most users will have familiarity with these modes and formats, you raise an excellent point with respect to columns that are included in multiple formats. In cases where a user requests more than one mode through the get_data method, including the modality as a prefix or suffix seems appropriate. I will make this change over the next few days.

I also very much appreciate the issues you opened in the ndbc-api repository, the suggestions and samples were excellent.

[ks905383]

Great! I only have two minor comments left (listed below), otherwise I recommend acceptance. Thanks for the work - it's always great to improve access to the often very janky online datastores of climate datasets....

1. Could you add conda/mamba install instructions to the README? Since it's on conda-forge anyways, might as well advertise it.
2. Would you consider making python 3.13 supported? I don't think too much changed that would mess with dependencies / tests (though would be easy to check by running the test package on 3.13 as well), but empty new environments are installing that python version, and if ndbc-api isn't specified in the initial environment, it'll install an older version instead (presumably the last one that didn't explicitly specify python requirements).

[CDJellen]

Thank you @ks905383 ! I've updated the README with conda instructions; great point there as this was a relatively recent change.

With respect to python 3.13 support, I've spent some time investigating this but it seems some dependencies (at least as reported through poetry) lack support for a wide enough version set. With that said, I've updated CI to include python 3.12 support in tests, and updated the package dependencies for 3.12 compatibility.

I will revisit support for 3.13 in a few weeks once the package dependencies have more recent updates.

Once again, thank you for taking the time to review and offer feedback on the package. Your suggestions were excellent, the migration to xarray is especially useful given how much cleaner that API is when compared to netCDF4. Have an excellent rest of your day!

[ks905383]

Great, @cheginit that concludes my review, I recommend acceptance.

[cheginit]

@ks905383 Thanks for your time and efforts in reviewing the submission and providing constructive comments, appreciate it!

[rwegener2]

@cheginit thanks for the reminder and sorry for the delay. I'll wrap this up by end of day tomorrow.

[rwegener2]

Hi @CDJellen, this is a great package you've built! Python-based access to NDBC data will help lots of folks use their data more easily.

I have comments on two aspects of this project so far:

Tests

• When I run the tests I get 21 passed, 99 skipped, and 1 warning. The only two test files that ran were tests/config/test_config.py and tests/test_ndbc_api.py. Is there a reason most of the tests are skipping, or am I making a mistake in how I'm running them?

Paper

Well written paper! A few points of feedback:

• Line 10: The phrase "file-based access methods" confused me a bit, but made more sense once I looked at your code. To make this clearer from the perspective of someone only reading the paper I suggest either 1) framing the challenge with the "file-based methods" as the fact that NDBC only provides an API but no Python wrapper and/or that the ASCII text files are not easy to parse, or 2) specifying in the next sentence that this package provides a user-friendly Python API that provides direct access to data as Python data structures.
• Line 26: You're addressing an important problem here but I think it gets glazed over in "the mode of access adds cost and complexity to their workflows". I'd either clarify how the current system adds cost (or remove that part) and also specify how it adds complexity. Personally, I would also note that there isn't a Python interface, only an API (as I understand it), downloading otherwise happens in a GUI, and that it is difficult to parse the text files.
• Line 29: typo "these critical gap"
• Line 33: I struggle with the word "modalities" as it is quite vague. I suggest either 1) after the word modalities include examples or a definition (maybe: "... stations, data modalitites (ex. wind speed, ocean temperature, etc.), ..." or 2) switching to another word/phrase such as 'data variables' or 'measurements'
• Line 34: with the suggestion from the previous reviewer should an xarray DataSet also be part of this list or objects?
• Line 34: The pandas team requests that you include the zenodo repository in addition to the McKinney article when citing pandas https://pandas.pydata.org/about/citing.html
• Line 47: typo, missing 'and' in "... their teams, their network ..."

[CDJellen]

Thank you so much for the feedback @rwegener2 ; I will work to address your comments on the paper over the next two days and update this PR once those changes are ready.

In terms of test coverage, some tests are expensive to run or test private methods. In order to get a good sense of the CI covrage, tests can be run with pytest using the --run-slow and --run-private flags. These gate the vast majority of the tests. Tests must pass in order for a PR to merge to main.

I very much appreciate your time and assistance in improving the paper; have an excellent rest of your day.

[CDJellen]

Thank you so much @cheginit ! I really appreciate your time throughout this process. The package is in much better shape thanks to the thoughtful reviews provided by @ks905383 and @rwegener2.

[kthyng]

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

• Are checklists all checked off?
• Check that version was updated and make sure the version from JOSS matches github and Zenodo.
• Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
• Check paper.

[kthyng]

Everything looks ready to go!

[kthyng]

@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: Jellen
  given-names: Christopher David
  orcid: "https://orcid.org/0000-0003-0469-353X"
doi: 10.5281/zenodo.14261355
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jellen
    given-names: Christopher David
    orcid: "https://orcid.org/0000-0003-0469-353X"
  date-published: 2024-12-04
  doi: 10.21105/joss.07406
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7406
  title: "ndbc-api: Accelerating oceanography and climate science
    research with Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07406"
  volume: 9
title: "`<code>`{=html}ndbc-api`</code>`{=html}: Accelerating
  oceanography and climate science research with Python"

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.

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[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🦋🦋🦋 👉 Bluesky post 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.07406 joss-papers#6217
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07406
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...

[kthyng]

@CDJellen Can you remove the "code" bits around "ndbc" in your title (ndbc-api)? They are not being rendered properly in our system.

[CDJellen]

@CDJellen Can you remove the "code" bits around "ndbc" in your title (ndbc-api)? They are not being rendered properly in our system.

Thank you for pointing this out @kthyng ; I've pushed the change. Please let me know if there is anything else I can do to assist, and have an excellent rest of your day!

[kthyng]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[kthyng]

Hm maybe I just need to reaccept...

[kthyng]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

⚠️ Couldn't update published paper. An error happened.

[kthyng]

hm I am not sure what is wrong. @openjournals/dev Could you help here?

[xuanxu]

@kthyng there was a conflict with an existing branch, please try the reaccept command again

[kthyng]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#6231

[kthyng]

thanks @xuanxu! Everything looks correct now!

Congratulations on your new publication @CDJellen! Many thanks to editor @cheginit and to reviewers @rwegener2 and @ks905383 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Note we have a new tool for reviewers! You can go to https://joss.theoj.org/papers/reviewed_by/@your-github-username to see the JOSS submissions you have reviewed, and you can also copy a badge there with the number of your JOSS reviews.

[editorialbot]

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[CDJellen]

Thank you again @cheginit , @ks905383 , @rwegener2, and @kthyng for your time and assistance in improving and publishing the manuscript! The process was nothing short of excellent from a submitter's perspective.

The review process lead to a significant number of technical improvements, as well as a dramatic improvement in the quality of the documentation.

I've signed up as a reviewer through the web portal; if there is anything I can do to assist in the future please let me know!

[kthyng]

@CDJellen Wonderful to hear!