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[REVIEW]: ndbc-api: Accelerating oceanography and climate science research with Python #7406

Open editorialbot opened 4 weeks ago

editorialbot commented 4 weeks ago

Submitting author: !--author-handle-->@CDJellen<!--end-author-handle-- (Chris Jellen) Repository: http://github.com/cdjellen/ndbc-api Branch with paper.md (empty if default branch): user/cjellen/joss-paper-submission Version: v2024.08.31.1 Editor: !--editor-->@cheginit<!--end-editor-- Reviewers: @rwegener2, @ks905383 Archive: Pending

Status

status

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HTML: <a href="https://joss.theoj.org/papers/7650fcdcf5309f37067b9f271f12e438"><img src="https://joss.theoj.org/papers/7650fcdcf5309f37067b9f271f12e438/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7650fcdcf5309f37067b9f271f12e438/status.svg)](https://joss.theoj.org/papers/7650fcdcf5309f37067b9f271f12e438)

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

@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. First of all you need to run this command in a separate comment to create the 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 commented 4 weeks 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:

@editorialbot commands

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 4 weeks ago

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 commented 4 weeks ago 
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 commented 4 weeks ago

Paper file info:

📄 Wordcount for paper.md is 600

✅ The paper includes a Statement of need section

editorialbot commented 4 weeks ago

License info:

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

cheginit commented 4 weeks ago

👋🏼 @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.

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editorialbot commented 4 weeks ago

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

ks905383 commented 4 weeks ago

Review checklist for @ks905383

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rwegener2 commented 3 weeks ago

Review checklist for @rwegener2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

cheginit commented 1 week ago

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

ks905383 commented 1 week ago

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

ks905383 commented 1 week ago
Bildschirmfoto 2024-11-13 um 4 00 20 PM

@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 commented 3 days ago

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 commented 3 days ago

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 commented 2 days ago

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 commented 1 day ago

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

cheginit commented 1 day ago

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

rwegener2 commented 1 day ago

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

rwegener2 commented 22 hours ago

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

Paper

Well written paper! A few points of feedback: