[REVIEW]: chombo-discharge: An AMR code for gas discharge simulations in complex geometries

[editorialbot]

Submitting author: @rmrsk (Robert Marskar)
Repository: https://github.com/chombo-discharge/chombo-discharge
Branch with paper.md (empty if default branch): joss
Version: <v23.05>
Editor: @ppxasjsm
Reviewers: @jannisteunissen, @michellegurevich
Archive: 10.5281/zenodo.7950220

Status

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Markdown: [![status](https://joss.theoj.org/papers/8faaa821cbb8065f6af7898e970766a5/status.svg)](https://joss.theoj.org/papers/8faaa821cbb8065f6af7898e970766a5)

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

@jannisteunissen & @michellegurevich, 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 @ppxasjsm 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 @jannisteunissen

📝 Checklist for @michellegurevich

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.68 s (1151.1 files/s, 265258.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                             242          15691           8282          56524
C/C++ Header                    309          11749          30693          31622
TeX                              35            567            368           4032
reStructuredText                 50           3633           3373           4032
JSON                              7              8              0           2646
INI                              10            550              0           1602
Python                           37            383            336           1568
Markdown                         55            415              0            809
YAML                              6             95              5            547
make                             28            182            133            479
Bourne Again Shell                2             18             30             36
CSS                               1              3              2             22
Bourne Shell                      1              0              0              5
--------------------------------------------------------------------------------
SUM:                            783          33294          43222         103924
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 731

[editorialbot]

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

OK DOIs

- 10.1016/j.jcp.2019.03.036 is OK
- 10.1088/0022-3727/42/19/194012 is OK
- 10.1088/1361-6595/abefa6 is OK
- 10.1109/TPS.2021.3120507 is OK
- 10.1088/1361-6463/aa8faf is OK
- 10.1088/1361-6595/aca0be is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[ppxasjsm]

Hi @jannisteunissen and @michellegurevich, you can now start the review process. If you have any questions please just give me a shout and I'll be happy to assist.

[jannisteunissen]

Review checklist for @jannisteunissen

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/chombo-discharge/chombo-discharge?
• 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 (@rmrsk) 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?

[michellegurevich]

Review checklist for @michellegurevich

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/chombo-discharge/chombo-discharge?
• 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 (@rmrsk) 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?

[ppxasjsm]

@jannisteunissen and @michellegurevich, I am just checking in about the review. Is everything going ok? Looks like you have already made quite some progress.

[michellegurevich]

Yes, all good on my end. I am hoping to finish early this week!

[michellegurevich]

I have completed reviewing the code. I have notified the author of a couple of suggestions around the installation, and he has made changes to provide additional information helpful for users in the documentation.

[ppxasjsm]

@michellegurevich brilliant thank you! @jannisteunissen could you give me an estimate for when you think you will be able to finish your review?

[jannisteunissen]

@michellegurevich brilliant thank you! @jannisteunissen could you give me an estimate for when you think you will be able to finish your review?

I'm back from holidays and will finish it by next week

[jannisteunissen]

I am now also done with my checklist (and have exchanged several messages with the author in the process).

[ppxasjsm]

@jannisteunissen Are you happy with everything? Or are there some remaining things that need to be addressed?

[jannisteunissen]

@ppxasjsm Yes happy with everything!

[rmrsk]

@ppxasjsm All good, or something else needed on my part?

[ppxasjsm]

Hi @rmrsk, I have to check through everything still. I've been at a conference but will hopefully get to it this week. apologies for the delay!

[ppxasjsm]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[ppxasjsm]

@rmrsk, can you please go through the additional author tasks listed above? If something is unclear do let me know.

[ppxasjsm]

I'll go through the paper now and will potentially make some minor suggestions.

[rmrsk]

@ppxasjsm Here is the extra information:

Release version: v23.05
DOI: 10.5281/zenodo.7950220

Regarding license: Could not find GPL-3.0 in the dropdown list on Zenodo but the guidelines says to choose "other", and include the LICENSE file with the archived files. Which I've done.

Edit: For some reason I can't check the boxes in the "Additional Author Tasks...." list

[ppxasjsm]

Yeah I don't think it contains a GPL-3 option. I have used GPL-2 or later as an option before, but including your file should be fine.

Thanks for creating the release version and archive!

[kyleniemeyer]

Hi @rmrsk, I made some minor edits to the paper in chombo-discharge/chombo-discharge#332

Can you review and merge this PR? We can then finish the publication process.

[rmrsk]

@kyleniemeyer Done.

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@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: Marskar
  given-names: Robert
  orcid: "https://orcid.org/0000-0003-1706-9736"
doi: 10.5281/zenodo.7950220
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Marskar
    given-names: Robert
    orcid: "https://orcid.org/0000-0003-1706-9736"
  date-published: 2023-05-22
  doi: 10.21105/joss.05335
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5335
  title: "chombo-discharge: An AMR code for gas discharge simulations in
    complex geometries"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05335"
  volume: 8
title: "chombo-discharge: An AMR code for gas discharge simulations in
  complex geometries"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.05335 joss-papers#4252
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05335
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...

[kyleniemeyer]

Congratulations @rmrsk on your article's publication in JOSS!

If you haven't already, please consider signing up as a reviewer to help pay it forward for future authors: https://reviewers.joss.theoj.org/join

Many thanks to @jannisteunissen and @michellegurevich for reviewing this, and @ppxasjsm for editing.

[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.05335/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05335/status.svg
   :target: https://doi.org/10.21105/joss.05335

This is how it will look in your documentation:

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[rmrsk]

@kyleniemeyer Did you forget to take out the section with the AAS article. This paper is not linked with any AAS submission.

[kyleniemeyer]

@rmrsk Oh, apologies, I missed that—not sure why that was in the paper to begin with.

[kyleniemeyer]

@rmrsk Please merge chombo-discharge/chombo-discharge#334 (or remove the header material yourself)

[kyleniemeyer]

@editorialbot generate pdf

[rmrsk]

@kyleniemeyer Done. I don't know either, it popped up at some point.

[kyleniemeyer]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

⚠️ An error happened when generating the pdf.

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4255

[kyleniemeyer]

@rmrsk ok, it looks like the paper PDF has been updated (https://www.theoj.org/joss-papers/joss.05335/10.21105.joss.05335.pdf); the cached version at https://doi.org/10.21105/joss.05335 might take a bit longer to reflect the correction.

[rmrsk]

Great! Thanks for the rapid response!