[REVIEW]: ncompare: A Python package for comparing netCDF structures

[editorialbot]

Submitting author: !--author-handle-->@dkauf42<!--end-author-handle-- (Daniel E Kaufman) Repository: https://github.com/nasa/ncompare Branch with paper.md (empty if default branch): joss-paper Version: v1.9.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @cmtso, @cmarmo Archive: 10.5281/zenodo.11448464

Status

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HTML: <a href="https://joss.theoj.org/papers/c12f4805d34b49fe4f814b2639fdfc96"><img src="https://joss.theoj.org/papers/c12f4805d34b49fe4f814b2639fdfc96/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c12f4805d34b49fe4f814b2639fdfc96/status.svg)](https://joss.theoj.org/papers/c12f4805d34b49fe4f814b2639fdfc96)

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

@cmtso & @cmarmo, 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

@cmtso, please create your checklist typing: @editorialbot generate my checklist

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[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 1.90  T=0.03 s (1451.3 files/s, 155143.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            273            266           1063
Markdown                         9            186              0            714
YAML                            10             52             56            328
Jupyter Notebook                 2              0            700            192
TeX                              1              1              0            129
CSV                              1              0              0            103
TOML                             1              9              3             75
CSS                              1              0              0             19
-------------------------------------------------------------------------------
SUM:                            39            521           1025           2623
-------------------------------------------------------------------------------

Commit count by author:

   282  danielfromearth
   152  ncompare bot
    59  dependabot[bot]
    33  Daniel Kaufman

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.7112925 is OK
- 10.1063/1.4823180 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5334/jors.148 is OK
- 10.1109/38.56302 is OK

MISSING DOIs

- No DOI given, and none found for title: Python 3 Reference Manual
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: Python: A dynamic, open source programming languag...
- No DOI given, and none found for title: TEMPO geolocated Earth radiances (BETA)

INVALID DOIs

- https://doi.org/10.1016/j.envsoft.2008.03.004 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jqsrt.2016.05.008 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 939

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[arfon]

@editorialbot assign 10.5281/zenodo.10625407 as archive

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[arfon]

@editorialbot set 10.5281/zenodo.10625407 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10625407

[editorialbot]

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

[arfon]

@dkauf42 – this is pretty much ready to go once the license issue mentioned in the pre-review thread is dealt with.

[danielfromearth]

Thanks @arfon! I'm checking with some NASA Langley folks to confirm software assurance requirements regarding the license.

[danielfromearth]

My apologies for the delay, @arfon. The software has now been approved to use the Apache License 2.0, so I will be changing the license file completely. I think this will be even better for the openness of this project. Will let you know when I have completed the changover.

[danielfromearth]

@arfon, although the license has been approved, there is still ongoing discussion regarding the copyright headers for source files. Sorry for the continued delay.

[danielfromearth]

@arfon, thank you very much for your patience as the license and copyright questions were addressed!

ncompare — now bumped to version 1.9.0 — has been re-licensed under the Apache License 2.0, and a LICENSE file has been placed in the root directory of the repository. I hope that both addresses the license discoverability issue and improves the openness of this ncompare code.

Please let me know if there is anything else I can do to help move this submission review to the next steps.

[arfon]

@editorialbot set v1.9.0 as version

[editorialbot]

Done! version is now v1.9.0

[arfon]

Thanks @danielfromearth – this sounds great. Can you make a new Zenodo release for this updated version please and let me know the DOI of that release here?

[danielfromearth]

@arfon, I just created a new release for version 1.9.0 with a DOI of <10.5281/zenodo.11448464>.

[arfon]

@editorialbot set 10.5281/zenodo.11448464 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11448464

[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

- 10.5281/zenodo.7112925 is OK
- 10.1063/1.4823180 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5334/jors.148 is OK
- 10.1109/38.56302 is OK

MISSING DOIs

- No DOI given, and none found for title: Python 3 Reference Manual
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: Python: A dynamic, open source programming languag...
- No DOI given, and none found for title: TEMPO geolocated Earth radiances (BETA)

INVALID DOIs

- https://doi.org/10.1016/j.envsoft.2008.03.004 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jqsrt.2016.05.008 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.envsoft.2008.03.004' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.
Element doi: [facet 'pattern'] The value 'https://doi.org/10.1016/j.jqsrt.2016.05.008' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

[arfon]

@danielfromearth – nearly there! This PR should fix those errors: https://github.com/nasa/ncompare/pull/228

[danielfromearth]

Merged — and thanks for opening the PR!

[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

- 10.5281/zenodo.7112925 is OK
- 10.1063/1.4823180 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5334/jors.148 is OK
- 10.1109/38.56302 is OK
- 10.1016/j.envsoft.2008.03.004 is OK
- 10.1016/j.jqsrt.2016.05.008 is OK

MISSING DOIs

- No DOI given, and none found for title: Python 3 Reference Manual
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: Python: A dynamic, open source programming languag...
- No DOI given, and none found for title: TEMPO geolocated Earth radiances (BETA)

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5460, 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...

[danielfromearth]

👋 @openjournals/dsais-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#5460, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@arfon, the proof link doesn't seem to work here. Does it work for you?

[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: Kaufman given-names: Daniel E. orcid: "https://orcid.org/0000-0002-1487-7298" - family-names: Baskin given-names: Walter E. orcid: "https://orcid.org/0000-0002-2241-3266" doi: 10.5281/zenodo.11448464 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Kaufman given-names: Daniel E. orcid: "https://orcid.org/0000-0002-1487-7298" - family-names: Baskin given-names: Walter E. orcid: "https://orcid.org/0000-0002-2241-3266" date-published: 2024-06-06 doi: 10.21105/joss.06490 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 6490 title: "ncompare: A Python package for comparing netCDF structures" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06490" volume: 9 title: "ncompare: A Python package for comparing netCDF structures" ```

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 :point_right: https://github.com/openjournals/joss-papers/pull/5461
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06490
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]

@cmtso, @cmarmo – 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 ✨

@danielfromearth – your paper is now accepted and published in JOSS :zap::rocket::boom:

[editorialbot]

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[danielfromearth]

@cmtso, @cmarmo – 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 ✨

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

Yay! We really appreciate you dedicating time and effort toward reviewing this paper, and for your patience during the process!