[REVIEW]: RESOURCECODE: A Python package for statistical analysis of sea-state hindcast data

[editorialbot]

Submitting author: @NRaillard (Nicolas Raillard)
Repository: https://gitlab.ifremer.fr/resourcecode/resourcecode
Branch with paper.md (empty if default branch): joss_paper
Version: 1.0.0
Editor: @marcosvital
Reviewers: @krober10nd, @platipodium, @malmans2
Archive: 10.5281/zenodo.7681494

Status

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Markdown: [![status](https://joss.theoj.org/papers/e43574f4a0b6782ee6a112180912dae0/status.svg)](https://joss.theoj.org/papers/e43574f4a0b6782ee6a112180912dae0)

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

@krober10nd & @platipodium & @malmans2, 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 @marcosvital 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

📝 Checklist for @krober10nd

[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=0.16 s (403.7 files/s, 44325.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          37            788           1585           2024
JSON                             4              0              0           1015
XML                              1              0              2            441
Markdown                         3            121              0            338
YAML                             2             18              0            142
reStructuredText                11             84             67            131
INI                              3             10              0             62
TeX                              1              7              1             62
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            63           1032           1662           4224
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1016/j.oceaneng.2019.05.016 is OK
- 10.1016/j.oceaneng.2013.04.015 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1099

[editorialbot]

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

[marcosvital]

Dear @krober10nd, @platipodium and @malmans2, thank you again for accepting review this submission for JOSS. The reviewing process is checklist based, and instructions were already posted above by the editorial bot - but let me know if you need any assistance, ok? Also, you can tag @NRaillard if you have specific questions about the manuscript.

@NRaillard, you can tag any of your co-authors if you want, so they would be able to follow this issue.

[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://gitlab.ifremer.fr/resourcecode/resourcecode?
• 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 (@NRaillard) 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

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 and who the target audience is?
• 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]

@NRaillard please provide instructions on how / login to to create issues in your upstream repo.

[platipodium]

The repository's author report is as follows:

Author	Commits (%)	+ lines	- lines	First commit	Last commit	Age	Active days	# by commits
Simon Chabot	138 (65.09%)	307176	249010	2020-07-23	2021-11-23	487 days, 23:04:26	46	1
RAILLARD	41 (19.34%)	1915	600	2021-11-24	2022-03-25	121 days, 1:12:41	5	2
Noe Gaumont	16 (7.55%)	44869	466	2021-08-26	2021-09-16	21 days, 1:31:28	5	3
ogiorgis	12 (5.66%)	2884	1277	2021-07-07	2021-07-13	5 days, 21:26:16	4	4
Nicolas RAILLARD	3 (1.42%)	3	3	2022-01-25	2022-01-25	0:16:07	1	5

The authors on the paper, however, are Nicolas Raillard1¶ , Christophe Maisondieu1 , David Darbynian2 , Gregory Payne∗ 3 , and Louis Papillon

There is some inconsistency in authorship and attributed that blocks acceptance and need to be better explained/corrected.

• The submitting author @NRaillard contributed 20% to the software, but is the sole author named in citation.cff
• Simon Chabot as the main contributor to source is not acknowledged anywhere, neither is Noe Guamont or ogiorgis
• The contribution role of Maisondieu, Darwinian, Panye and Papillon is not clear

[NRaillard]

Hello @platipodium thanks for taking some time for the review.

To login on our self-hosted gitlab instance, I need to create an account: I just need your name and email address to do so. I can do also for @krober10nd and @malmans2 as soon as they send me the requested information (by mail or DM)

To clarify the authorship, some of the modules were converted from matlab, Fortran and R codes developed by the authors (C. Maisondieu, D. Darbynian, G. Payne, L. Papillon and myself) as part of a subcontracting to develop the python package. Most of the authors do not use git so do not appear in the aforementioned report but made the most significant contribution to the project.

However, looking at the table, it is clear that Simon Chabot did the most part of the job and should be credited for that, even if the copyright is transfered to IFREMER. I will see with him if he want to be credited and modify the paper accordingly.

[platipodium]

Thank you @NRaillard for starting to answer the authorship issue. Let's continue this in your repository once we all register there. We will have to talk about the separate issues of (1) Copyright and (2) Intellectual property. Also note that in the current code there remain about 50 k lines form Simon and 50 k lines from Noe, and about 2 k from yourself and ogiorgis.

[malmans2]

Review checklist for @malmans2

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://gitlab.ifremer.fr/resourcecode/resourcecode?
• 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 (@NRaillard) 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

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 and who the target audience is?
• 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]

• Issue https://gitlab.ifremer.fr/resourcecode/resourcecode/-/issues/8 on copyright

[platipodium]

• Issue https://gitlab.ifremer.fr/resourcecode/resourcecode/-/issues/9 on authorship

[platipodium]

• Issue https://gitlab.ifremer.fr/resourcecode/resourcecode/-/issues/10 on missing community guidelines

[NRaillard]

@editorialbot generate pdf

[editorialbot]

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

[NRaillard]

@editorialbot generate pdf

[editorialbot]

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

[platipodium]

[ ] Issue https://gitlab.ifremer.fr/resourcecode/resourcecode/-/issues/10 on missing community guidelines

Contribution copyright retention / transfer not yet resolved. Please make clear how you would like to accept contributions. Read all about pros and cons at http://harmonyagreements.org/index.html

[marcosvital]

Dear @krober10nd, I noticed that you still don't have a reviewing checklist yet, so I'm not sure if you already had the chance to start revising this submission. Let me know if you have any problems and if you believe that you can start that soon, ok?

[krober10nd]

Review checklist for @krober10nd

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://gitlab.ifremer.fr/resourcecode/resourcecode?
• 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 (@NRaillard) 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

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?

[krober10nd]

@marcosvital I'll get started in the next week. Sorry for the delay.

[marcosvital]

@marcosvital I'll get started in the next week. Sorry for the delay.

No problem, and thank you for letting us know.

[platipodium]

• Installation fails on aarch64-conda-py3.10 https://gitlab.ifremer.fr/resourcecode/resourcecode/-/issues/13

[kthyng]

Ok everything looks good! I will run final acceptance.

[kthyng]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

⚠️ Couldn't acccept/publish paper. An error happened.

[kthyng]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

⚠️ Couldn't acccept/publish paper. An error happened.

[kthyng]

@openjournals/dev I took a look at the errors and I don't see an obvious issue with the paper. Is something else going on?

[xuanxu]

There's been an error in a post acceptance task, but the paper has been correctly accepted an deposited.
The DOI is 10.21105/joss.04366

[kthyng]

@xuanxu Ok, is there something I can do to wrap up this review issue or should I wait and try again later?

[xuanxu]

I've added the accepted label so closing the issue will wrap it up.

[kthyng]

Ok great, thanks!

It's a little anti-climactic without the text that usually comes up upon acceptance, but congrats on your new publication @NRaillard! Many thanks to editor @marcosvital and reviewers @krober10nd, @platipodium, and @malmans2 for your time, hard work, and expertise!!

[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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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04366/status.svg
   :target: https://doi.org/10.21105/joss.04366

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[NRaillard]

Many thanks to @marcosvital for editing this paper, and of course to the reviewers @krober10nd @platipodium and @malmans2 that provide me with very good comments to ensure the quality of the package and to improve the documentation.

Thanks all to @kthyng and the the whole JOSS team (and the @editorialbot ;) ) for the great submission experience (I just hope I will not miss the corresponding tweet to make some ad about this publication ;) ).

Looking forward conducting reviews and sending further papers !

[kthyng]

@Kevin-Mattheus-Moerman Looks like you are in charge of the JOSS twitter account — could you make tweet about this paper? There was an error in the final publication process such that while the paper was published, some of the other steps didn't occur.

[xuanxu]

Here are the Twitter and Mastodon posts:

🐦 🐦 🐦 Tweet for this paper 🐦 🐦 🐦
🐘 🐘 🐘 Toot for this paper 🐘 🐘 🐘

[NRaillard]

That's neat !
Thanks @xuanxu !