[REVIEW]: NcCut: A NetCDF Viewer and Transecting Tool

[editorialbot]

Submitting author: @rchartra (Robin Chartrand)
Repository: https://github.com/rchartra/NcCut
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @hugoledoux
Reviewers: @platipodium, @Huite
Archive: 10.5281/zenodo.14862691

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/078dcd397b81d435fce2bf9e78431dcd"><img src="https://joss.theoj.org/papers/078dcd397b81d435fce2bf9e78431dcd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/078dcd397b81d435fce2bf9e78431dcd/status.svg)](https://joss.theoj.org/papers/078dcd397b81d435fce2bf9e78431dcd)

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

@platipodium & @Huite, 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 @hugoledoux 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 @Huite

[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]

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

✅ OK DOIs

- 10.1029/2021JC018075 is OK
- 10.5194/os-17-1421-2021 is OK
- 10.5281/zenodo.5625933 is OK
- 10.5281/zenodo.7897029 is OK
- 10.5281/zenodo.5176030 is OK
- 10.5281/zenodo.10199 is OK
- 10.5281/zenodo.5869838 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Panoply Data Viewer
- No DOI given, and none found for title: Ncview

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (733.7 files/s, 240817.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             8           1492             26           8695
SVG                              1              0              0           2671
Python                          18            602           1313           2592
CSS                              6            339             51           1324
JavaScript                      12            138            228            912
reStructuredText                11            244            114            362
Markdown                         2             54              0            175
YAML                             3             12              0            139
TeX                              1              8              0             85
TOML                             1              6              0             45
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            288             19
make                             1              4              7              9
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            67           2907           2028          17055
-------------------------------------------------------------------------------

Commit count by author:

   284	rchartra
    14	github-actions[bot]

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1008

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[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/rchartra/NcCut?
• 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 (@rchartra) 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]

@rchartra I had severe trouble with the usability of the interface. I filed an issue only giving a glimpse into those troubles; you may seek help and other opinions to move this project forward.

[Huite]

Review checklist for @Huite

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/rchartra/NcCut?
• 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 (@rchartra) 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?

[hugoledoux]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[hugoledoux]

@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

- 10.1029/2021JC018075 is OK
- 10.5194/os-17-1421-2021 is OK
- 10.5281/zenodo.5625933 is OK
- 10.5281/zenodo.7897029 is OK
- 10.5281/zenodo.5176030 is OK
- 10.5281/zenodo.10199 is OK
- 10.5281/zenodo.5869838 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Panoply Data Viewer
- No DOI given, and none found for title: Ncview

❌ MISSING DOIs

- None

❌ 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#6429, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[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]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.06 s (768.6 files/s, 153384.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22            839           2028           4162
kvlang                           3             85             10            566
reStructuredText                 7            169             96            257
YAML                             3             15              3            236
Markdown                         2             53              0            173
Text                             3             14              0            121
TeX                              1              8              0             85
TOML                             3             14              7             66
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            298             19
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            47           1209           2450           5720
-------------------------------------------------------------------------------

Commit count by author:

   392	rchartra
    22	github-actions[bot]
     1	Hugo Ledoux

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1078

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 Failed to discover a valid open source license

[kthyng]

@rchartra Looks like a CC license has been added to the repository — Can you update me on the reasoning? CC is not an open source license.

[kthyng]

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

[rchartra]

The CC0 1.0 license was recommended to me as being better suited for images. As such per my REUSE.toml configuration only those files are covered by the CC0 1.0 license while all code is covered by the BSD-3 license

[rchartra]

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

Fixed!

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

Ok 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: Chartrand
  given-names: Robin
  orcid: "https://orcid.org/0000-0001-6948-8380"
- family-names: Fajber
  given-names: Robert
  orcid: "https://orcid.org/0000-0002-4656-7163"
- family-names: Manucharyan
  given-names: Georgy
  orcid: "https://orcid.org/0000-0001-7959-2675"
doi: 10.5281/zenodo.14862691
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Chartrand
    given-names: Robin
    orcid: "https://orcid.org/0000-0001-6948-8380"
  - family-names: Fajber
    given-names: Robert
    orcid: "https://orcid.org/0000-0002-4656-7163"
  - family-names: Manucharyan
    given-names: Georgy
    orcid: "https://orcid.org/0000-0001-7959-2675"
  date-published: 2025-02-24
  doi: 10.21105/joss.07185
  issn: 2475-9066
  issue: 106
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7185
  title: "NcCut: A NetCDF Viewer and Transecting Tool"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07185"
  volume: 10
title: "NcCut: A NetCDF Viewer and Transecting Tool"

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]

🦋🦋🦋 👉 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.07185 joss-papers#6453
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07185
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]

Congratulations on your new publication @rchartra! Many thanks to editor @hugoledoux and to reviewers @platipodium and @Huite 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.

@rchartra If you'd like to join JOSS as a reviewer, please sign up at https://reviewers.joss.theoj.org/join!

[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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07185/status.svg)](https://doi.org/10.21105/joss.07185)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07185">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07185/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07185/status.svg
   :target: https://doi.org/10.21105/joss.07185

This is how it will look in your documentation:

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