[REVIEW]: nctoolkit: A Python package for netCDF analysis and post-processing

[editorialbot]

Submitting author: @robertjwilson (Robert Wilson)
Repository: https://github.com/pmlmodelling/nctoolkit
Branch with paper.md (empty if default branch): joss-paper
Version: v1.0.0
Editor: @martinfleis
Reviewers: @malmans2, @platipodium
Archive: 10.5281/zenodo.8183367

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/06bcbb7e9aa80b276004b9445d6d4dbd"><img src="https://joss.theoj.org/papers/06bcbb7e9aa80b276004b9445d6d4dbd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/06bcbb7e9aa80b276004b9445d6d4dbd/status.svg)](https://joss.theoj.org/papers/06bcbb7e9aa80b276004b9445d6d4dbd)

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

@malmans2 & @platipodium, 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 @martinfleis 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 @platipodium

📝 Checklist for @malmans2

[editorialbot]

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:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.93 s (72.1 files/s, 24212.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         151           6556           3209          17086
reStructuredText                16            945            478            908
Jupyter Notebook                12              0          39913            350
TeX                              2             12              0            276
Bourne Shell                    15             75              8            222
YAML                             8             47             52            217
Markdown                         5            138              0            198
HTML                             2             70              0            138
-------------------------------------------------------------------------------
SUM:                           211           7843          43660          19395
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1002/joc.1169 is OK
- 10.5281/zenodo.7112925 is OK
- 10.5194/gmd-10-4619-2017 is OK
- 10.5334/jors.148 is OK
- 10.25080/majora-7b98e3ed-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5194/gmd-14-629-2021 is OK
- 10.5194/gmd-9-3461-2016 is OK
- 10.1038/d41586-018-05869-5 is OK

MISSING DOIs

- 10.1109/mcse.2007.55 may be a valid DOI for title: Matplotlib: A 2D graphics environment

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 948

[martinfleis]

👋🏼 @robertjwilson, @malmans2, @platipodium this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers should create checklists with the JOSS requirements using the command @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 small pull requests if needed) on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5494 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, feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

Thanks!

[editorialbot]

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

[platipodium]

Review checklist for @platipodium

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/pmlmodelling/nctoolkit?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@robertjwilson) 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?

[platipodium]

Explain why not use dask or similar tech: pmlmodelling/nctoolkit#57

[platipodium]

Discriminate from other software capabilities: pmlmodelling/nctoolkit#58

[platipodium]

Make sure summary targets lay audience: pmlmodelling/nctoolkit#59

[platipodium]

Portability problems to Mac running Monterey/Ventura python 3.10 + 3.11, see pmlmodelling/nctoolkit#29

[platipodium]

Documentation of cartopy dependency missing: pmlmodelling/nctoolkit#60

[platipodium]

Garbled plot from example: pmlmodelling/nctoolkit#61

[platipodium]

For better community integration, please consider the following:

• [JOSS] Add guidelines on how to contribute pmlmodelling/nctoolkit#62
• [JOSS] Add guideline for how to seek support / report problems pmlmodelling/nctoolkit#63

[platipodium]

Garbled plot from example: pmlmodelling/nctoolkit#61

I can't verify this until pmlmodelling/nctoolkit#29 is fixed

[editorialbot]

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

OK DOIs

- 10.1002/joc.1169 is OK
- 10.1029/2018MS001400 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.7112925 is OK
- 10.5194/gmd-10-4619-2017 is OK
- 10.5334/jors.148 is OK
- 10.25080/majora-7b98e3ed-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5194/gmd-14-629-2021 is OK
- 10.5194/gmd-9-3461-2016 is OK
- 10.1038/d41586-018-05869-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[martinfleis]

Thanks @robertjwilson! That is all from my side and the paper has been recommended for acceptance and handed over to the editor in chief for the final checks and publication.

[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#4457, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[robertjwilson]

Thanks for the editorial @martinfleis, and once again thanks to @platipodium and @malmans2 for their thorough and helpful reviews.

[kthyng]

• Check that version was updated
• Check that software archive exists, has been input to JOSS, and title and author list look good
• Check paper

[kthyng]

@robertjwilson Can you read through your paper carefully and make edits? I see a number in the first few paragraphs including needing a space between the sentence and the reference and spelling errors, and I bet you can catch them yourself without me detailing them. Please check the references too — python is sometime capitalized and sometimes not.

[robertjwilson]

Hi @kthyng

I have just made changes. Hopefully I haven't missed anything. References issues seem to be caused by not having double brackets around all titles, but that should now be fixed.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@robertjwilson can you do another check? Line 26: "rapdily"

[robertjwilson]

@kthyng Sorry. My bad. I ran it through Word and somehow didn't spot that and one other mistake. I have just updated it.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

Ok looks good. I'm interested in this package because I find nco tools difficult to use in terms of what command to use — maybe there are too many options!

[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: Wilson
  given-names: Robert J.
  orcid: "https://orcid.org/0000-0002-0592-366X"
- family-names: Artioli
  given-names: Yuri
  orcid: "https://orcid.org/0000-0002-5498-4223"
contact:
- family-names: Wilson
  given-names: Robert J.
  orcid: "https://orcid.org/0000-0002-0592-366X"
doi: 10.5281/zenodo.8183367
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Wilson
    given-names: Robert J.
    orcid: "https://orcid.org/0000-0002-0592-366X"
  - family-names: Artioli
    given-names: Yuri
    orcid: "https://orcid.org/0000-0002-5498-4223"
  date-published: 2023-08-09
  doi: 10.21105/joss.05494
  issn: 2475-9066
  issue: 88
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5494
  title: "nctoolkit: A Python package for netCDF analysis and
    post-processing"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05494"
  volume: 8
title: "nctoolkit: A Python package for netCDF analysis and
  post-processing"

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.05494 joss-papers#4463
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05494
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]

Congrats on your new publication @robertjwilson!! Many thanks to editor @martinfleis and reviewers @malmans2 and @platipodium for your hard work, time, and expertise!!

(I'll close this issue once the DOI resolves)

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05494/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05494/status.svg
   :target: https://doi.org/10.21105/joss.05494

This is how it will look in your documentation:

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