[REVIEW]: A C++ template library for polynomials algebra over discrete euclidean domains

[editorialbot]

Submitting author: @JeWaVe (regis portalez)
Repository: https://github.com/aerobus-open-source/aerobus
Branch with paper.md (empty if default branch):
Version: v1.4
Editor: @gkthiruvathukal
Reviewers: @mmoelle1, @lucaferranti, @pitsianis
Archive: 10.6084/m9.figshare.27517938

Status

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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

@mmoelle1 & @lucaferranti & @pitsianis, 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 @gkthiruvathukal 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 @pitsianis

📝 Checklist for @lucaferranti

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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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=0.04 s (293.4 files/s, 151843.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                     2            398            303           3611
C++                              2            151             53           1242
Markdown                         2            126              0            610
JSON                             3              0              0             85
CMake                            1              7              1             46
TeX                              1              2              0             32
YAML                             1              4              4             31
make                             1              7              0             15
-------------------------------------------------------------------------------
SUM:                            13            695            361           5672
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2506

[editorialbot]

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

OK DOIs

- 10.1007/978-3-319-06486-4_7 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[pitsianis]

Review checklist for @pitsianis

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/aerobus-open-source/aerobus?
• 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 (@JeWaVe) 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?

[pitsianis]

@JeWaVe, please make an extra effort to fix orthographic and syntactic mistakes in your paper.
There is no excuse now that ChatGPT, Grammarly, and other tools are widely available.
Please take a look at line 63.

If 𝔸 is euclidean, we can build it’s field of fractions: the smallest field containg 𝔸.

Please

• capitalize proper names like Euclid, Taylor
• do not use contractions like "it's"; it is too informal (for publications), and in this instance, it is also wrong
• use a spell checker and grammar helper to catch typos like "containg"
• consistently use mathematical expressions between dollar signs and program items between backquotes.
• use correct language annotations to highlight the assembly code blocks

Also, the list of citations needs to be more significant for such a rich field.

[JeWaVe]

Hi and thanks for the comments.
I tried to address them in my latest commit in main.

@editorialbot generate pdf

[JeWaVe]

@editorialbot generate pdf

[editorialbot]

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

[JeWaVe]

Just added missing reference @editorialbot generate pdf

[danielskatz]

@editorialbot generate pdf

A command needs to be the first thing in a new comment

[editorialbot]

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

[JeWaVe]

@editorialbot generate pdf
forgot to push the .bib file

[editorialbot]

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

[JeWaVe]

@editorialbot generate pdf
add missing references

freezing development - waiting for review

[editorialbot]

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

[danielskatz]

👋 @gkthiruvathukal - What's the status of this review? What needs to happen next?

[JeWaVe]

Well i need reviewers ;) Envoyé depuis Proton Mail mobile

…

-------- Message d'origine -------- Le 7 févr. 2024 à 22:14, Daniel S. Katz a écrit :

👋 ***@***.***(https://github.com/gkthiruvathukal) - What's the status of this review? What needs to happen next? — Reply to this email directly, [view it on GitHub](#6233 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/ACXJDMJOTXZC3GHDLIUNMDLYSPVDZAVCNFSM6AAAAABB5PYL5GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZSHEZDKNJUGQ). You are receiving this because you were mentioned.Message ID: ***@***.***>

[danielskatz]

@JeWaVe - yes, I know. But it's the job of the editor to find the reviewers, which is why I was pinging the editor in a friendly way. I don't know if he has been contacting potential reviewers outside of the issue, such as by email.

[gkthiruvathukal]

@danielskatz I am not sure whether something has gone wrong, we already have reviewers @mmoelle1, @lucaferranti, @pitsianis. However, we only seem to have a review checklist for @pitsianis. Do you have any idea what might be wrong here?

And apologies for the delays on my end. The past few weeks have been super busy with my chairperson duties. I'll try to keep the review moving.

[danielskatz]

I'm sorry @gkthiruvathukal - I seem to have misread the status here. I do now see that there are three reviewers assigned, and one has started their review. It seems that the other two reviewers have not yet started, meaning that they have not yet run the @editorialbot generate my checklist command. Hopefully, that will happen soon, so that the reviews can be completed in the six weeks that we ask for, which really means the next three weeks in this case.

[JeWaVe]

I did what you suggested : remove benchmarks from paper and replace them by a reference to a figshare csv file

[JeWaVe]

@editorialbot generate pdf

[editorialbot]

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

[gkthiruvathukal]

@lucaferranti and @pitsianis Have you been able to complete your reviews for this JOSS submission? Has your feedback been satisfactorily addressed?

[JeWaVe]

Ping. Why does it take so long ? Please tell me what is the status of this paper ?

[gkthiruvathukal]

@JeWaVe I am still waiting for the reviewers to respond. It seems like you have addressed all feedback.

[gkthiruvathukal]

@JeWaVe In looking through the feedback, I believe all points have been addressed. I'm going to proceed with generating the final checklist.

[gkthiruvathukal]

@editorialbot commands

[editorialbot]

Hello @gkthiruvathukal, here are the things you can ask me to do:

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# Adds a checklist for the reviewer using this command
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# Set a value for version
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[gkthiruvathukal]

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 pull request)
• 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

[gkthiruvathukal]

@JeWaVe Please do all of the above "additional author tasks" and let me know when complete.

[JeWaVe]

Hi,

here is the archive for the release : 10.6084/m9.figshare.27517938

License is MIT, same as for the code

Latest release is v1.4 (github and figshare)

[gkthiruvathukal]

@JeWaVe Thank you so much! I will get on the case after returning from my weekend trip.

[gkthiruvathukal]

@editorialbot set 10.6084/m9.figshare.27517938 as archive

[editorialbot]

Done! archive is now 10.6084/m9.figshare.27517938

[gkthiruvathukal]

@editorialbot set v1.4 as release

[editorialbot]

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

@editorialbot commands

[gkthiruvathukal]

@editorialbot generate pdf

[gkthiruvathukal]

@editorialbot set v1.4 as version

[editorialbot]

Done! version is now v1.4

[editorialbot]

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

[gkthiruvathukal]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/978-3-319-06486-4_7 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: vml: Vectorized Math Library
- No DOI given, and none found for title: On-Line Encyclopedia of Integer Sequences
- No DOI given, and none found for title: Algebra II: Chapters 4-7
- No DOI given, and none found for title: Mémoire sur les conditions de résolubilité des équ...
- No DOI given, and none found for title: Handbook of computational group theory
- No DOI given, and none found for title: The thirteen books of Euclid’s Elements
- No DOI given, and none found for title: A New Method of Solving Numerical Equations of all...
- No DOI given, and none found for title: Art of computer programming, volume 2: Seminumeric...
- No DOI given, and none found for title: Algorithms for geodesics
- No DOI given, and none found for title: Compensated horner scheme
- No DOI given, and none found for title: Aerobus benchmarks

❌ MISSING DOIs

- 10.1155/5708 may be a valid DOI for title: Algebra
- 10.1007/978-3-642-15582-6_5 may be a valid DOI for title: Sollya: An Environment for the Development of Nume...

❌ INVALID DOIs

- None

[gkthiruvathukal]

@JeWaVe Can you please check the missing DOIs in the above so I can finalize this submission? Thank you!

[JeWaVe]

Sure.

Algebra : https://doi.org/10.1007/978-1-4613-0041-0 (https://link.springer.com/book/10.1007/978-1-4613-0041-0)

Sollya : 10.1007/978-3-642-15582-6_5. (https://inria.hal.science/hal-00761644/document)

[gkthiruvathukal]

@editorialbot commands

[editorialbot]

Hello @gkthiruvathukal, here are the things you can ask me to do:

# List all available commands
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@editorialbot add @username as reviewer

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# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
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# Mention the EiCs for the correct track
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[gkthiruvathukal]

@JeWaVe Did you correct those DOIs in your paper submission?

[gkthiruvathukal]

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 pull request)
• 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

[gkthiruvathukal]

@JeWaVe See author tasks above. Please also confirm that your DOIs in the paper are all correct.