[REVIEW]: Snek5000: a new Python framework for Nek5000

[editorialbot]

Submitting author: @paugier (Pierre Augier)
Repository: https://github.com/snek5000/snek5000
Branch with paper.md (empty if default branch):
Version: v0.9.2
Editor: @philipcardiff
Reviewers: @joneuhauser, @maxhutch
Archive: 10.5281/zenodo.8278552

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/838e3330aa18e639f026658c718452f1"><img src="https://joss.theoj.org/papers/838e3330aa18e639f026658c718452f1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/838e3330aa18e639f026658c718452f1/status.svg)](https://joss.theoj.org/papers/838e3330aa18e639f026658c718452f1)

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

@joneuhauser & @maxhutch, 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 @philipcardiff 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 @joneuhauser

📝 Checklist for @maxhutch

[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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (1554.4 files/s, 144235.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           72           2034           2069           4795
Markdown                         34            657              0           1999
reStructuredText                 15            235            214            304
Fortran 77                        4             73             67            275
YAML                              9             47             25            266
TeX                               1             12              0            147
SVG                               1              0              0            120
TOML                              2             16             12             87
make                              3             27              9             71
JSON                              1              0              0             62
Bourne Again Shell                1              5              4             42
Bourne Shell                      2              3              2             40
HTML                              1              6              0             36
DOS Batch                         1              8              1             26
Nix                               1              3              2             21
CSS                               1              0              0              4
--------------------------------------------------------------------------------
SUM:                            149           3126           2405           8295
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1398

[editorialbot]

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

OK DOIs

- 10.5334/jors.237 is OK
- 10.5334/jors.239 is OK
- 10.5281/zenodo.7358961 is OK
- 10.12688/f1000research.29032.1 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5334/jors.148 is OK
- 10.1016/j.parco.2022.102982 is OK
- 10.1145/2938615.2938617 is OK
- 10.1145/3492805.3492818 is OK
- 10.1063/1.168744 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[joneuhauser]

Review checklist for @joneuhauser

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/snek5000/snek5000?
• 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 (@paugier) 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?

[philipcardiff]

Hi @joneuhauser, from your checklist, you seem to be happy with this contribution. If you have any additional comments, you can add them here or create an issue directly in the repository. Once everything is in order, you can confirm that you recommend acceptance here.

[joneuhauser]

@philipcardiff I have opened a few issues in the repository when I reviewed it last week. I'm not using this project regularly, so only what I found from review-related testing (i.e. trying out the tutorials).

I recommend acceptance in JOSS.

[philipcardiff]

Thanks @joneuhauser.

@paugier, you will see that four issues were opened by @joneuhauser:

• Phill example: Runtime error due to USERPARAM12 snek5000/snek5000#294
• Readme: points to plot_dt, which doesn't exist snek5000/snek5000#295
• Readme: error on history_points.plot() snek5000/snek5000#296
• Error when a line in the config file is commented out snek5000/snek5000#297

[ashwinvis]

FYI, @philipcardiff all the issues have been addressed.

[philipcardiff]

FYI, @philipcardiff all the issues have been addressed.

Thanks @ashwinvis .

@maxhutch: a short reminder.

[maxhutch]

Review checklist for @maxhutch

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/snek5000/snek5000?
• 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 (@paugier) 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?

[philipcardiff]

Hi @maxhutch, I see you mostly completed the reviewer checklist and the issue you raised (snek5000/snek5000#302) was resolved.

If you have any questions/comments regarding the final checklist points (Substantial scholarly effort, Functionality, and Functionality documentation), please raise them here or as an issue in the repository.

[maxhutch]

I recommend acceptance in JOSS as well.

[philipcardiff]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5334/jors.237 is OK
- 10.5334/jors.239 is OK
- 10.5281/zenodo.7358961 is OK
- 10.12688/f1000research.29032.1 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5334/jors.148 is OK
- 10.1016/j.parco.2022.102982 is OK
- 10.1145/2938615.2938617 is OK
- 10.1145/3492805.3492818 is OK
- 10.1063/1.168744 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[philipcardiff]

@editorialbot generate pdf

[editorialbot]

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

[philipcardiff]

Hi @paugier, @ashwinvis, please check the article again for any final changes. Once done, please issue a new tagged release of the software (if changed) and archive it (e.g. on Zenodo, figshare, or others). Please then post the version number and archive DOI here.

[ashwinvis]

@editorialbot set v0.9.2 as version

[editorialbot]

I'm sorry @ashwinvis, I'm afraid I can't do that. That's something only editors are allowed to do.

[ashwinvis]

@philipcardiff
The new version is v0.9.2 (or git tag 0.9.2)
I have also archived it to Zenodo (https://zenodo.org/record/8278552) (doi: 10.5281/zenodo.8278552)

[philipcardiff]

@editorialbot set 10.5281/zenodo.8278552 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8278552

[philipcardiff]

@editorialbot set v0.9.2 as version

[editorialbot]

Done! version is now v0.9.2

[philipcardiff]

@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

- 10.5334/jors.237 is OK
- 10.5334/jors.239 is OK
- 10.5281/zenodo.7358961 is OK
- 10.12688/f1000research.29032.1 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5334/jors.148 is OK
- 10.1016/j.parco.2022.102982 is OK
- 10.1145/2938615.2938617 is OK
- 10.1145/3492805.3492818 is OK
- 10.1063/1.168744 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/pe-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#4506, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[philipcardiff]

Hi @kyleniemeyer, this paper is ready for processing.

[kyleniemeyer]

Hi @paugier, I made a few small edits to the paper. Can you review and merge these? snek5000/snek5000#308

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

OK, all looks good to me now.

[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: Mohanan
  given-names: Ashwin Vishnu
  orcid: "https://orcid.org/0000-0002-2979-6327"
- family-names: Khoubani
  given-names: Arman
  orcid: "https://orcid.org/0000-0002-0295-5308"
- family-names: Augier
  given-names: Pierre
  orcid: "https://orcid.org/0000-0001-9481-4459"
doi: 10.5281/zenodo.8278552
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Mohanan
    given-names: Ashwin Vishnu
    orcid: "https://orcid.org/0000-0002-2979-6327"
  - family-names: Khoubani
    given-names: Arman
    orcid: "https://orcid.org/0000-0002-0295-5308"
  - family-names: Augier
    given-names: Pierre
    orcid: "https://orcid.org/0000-0001-9481-4459"
  date-published: 2023-08-24
  doi: 10.21105/joss.05586
  issn: 2475-9066
  issue: 88
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5586
  title: "Snek5000: a new Python framework for Nek5000"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05586"
  volume: 8
title: "Snek5000: a new Python framework for Nek5000"

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.05586 joss-papers#4508
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05586
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 @paugier on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @joneuhauser and @maxhutch for reviewing this, and @philipcardiff for editing.

[editorialbot]

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05586/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05586/status.svg
   :target: https://doi.org/10.21105/joss.05586

This is how it will look in your documentation:

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[paugier]

Thanks a lot @kyleniemeyer, @joneuhauser, @maxhutch and @philipcardiff for your work on JOSS and on this paper. The review process in JOSS is really a pleasant experience!

@ashwinvis and @akhoubani, we can be happy with this achievement. This was much harder than using Nek5000 with quick and dirty scripting but Snek5000 is a real added value in the long term. @akhoubani this is also a very good news for your PhD thesis!