[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: v1.1
Editor: @gkthiruvathukal
Reviewers: @mmoelle1, @lucaferranti, @pitsianis
Archive: Pending

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:

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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]

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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 moved tests to google tests in main branch.
Now : update readme + install / usage / tests instructions

[JeWaVe]

usage / tests / bench instructions updated -- should be oK now but didn't test on windows yet (I updated the cmakelists.txt)

[JeWaVe]

I'm extending and cleaning the documentation, sorry it's a long process

[JeWaVe]

It's now published at https://aerobus-open-source.github.io/aerobus/
README is updated an imported in documentation
added issue and PR template
I cleaned up the paper, tell me if I go in the right direction

@editorialbot generate pdf

[JeWaVe]

@editorialbot generate pdf

[editorialbot]

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

[gkthiruvathukal]

@JeWaVe Thanks for your work on this. We are heading in a promising direction!

@mmoelle1, @lucaferranti, @pitsianis: Can you let me know whether the latest changes are satisfactory? I'd like to move toward acceptance soon.

[lucaferranti]

@editorialbot generate pdf

[editorialbot]

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

[JeWaVe]

Hi,

I'm coming to the news. Did you get a chance to review the changes I made ? Are they satisfactory ?

Regards,

Regis Portalez

[gkthiruvathukal]

@mmoelle1, @lucaferranti, @pitsianis: Can you let me know whether the latest changes are satisfactory? I'd like to move toward acceptance soon.

[lucaferranti]

@editorialbot generate pdf

[editorialbot]

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

[lucaferranti]

Hi @JeWaVe (cc @gkthiruvathukal )

The repository looks much better now! Some comments:

• In the examples section of the documentation, there are several broken links (QuotientField, FractionField, PI_Fraction::val). For the working links, those seem more like API documentation and not example usages.
• Contributing guidelines are still missing

Also, my previous comment about the paper length remains open:

My main comment for the paper is that at the moment I think it does not conform to the JOSS format. Mainly, the paper is currently 12 pages, while generally JOSS expects a much shorter (~ 2 pages) paper, which should give a general motivation and overview of timeless features of the sofware. Currently, the paper presents several examples, background theory and code snippets, which I believe would better fit the documentation. The reason for this is that software can change and things written in the paper are frozen, while documentation can evolve and update (see also my comment on documentation below). However I let the editor decide and overwrite my comment if he thinks the paper is appropriate this way.

[JeWaVe]

Hi,

I added contributing guidelines and code of conduct.
I understood why examples are broken and that is because I misunderstood the @example tag. Going to fix them all now.

[pitsianis]

I am not satisfied with the changes. The draft has no coherent message; it is an enumeration of the contents of a bag of different things that only have in common that they have been included in the Aerobus macro library.

Let's start from the title, which specifies "polynomial algebra over discrete Euclidean domains", however The Statement of Need only dedicates a single line:

By implementing general algebra concepts such as discrete rings, field of fractions and polynomials, Aerobus can serve multiple purposes.

that says nothing to address the need for a polynomial algebra over discrete domains.

The rest of The Statement of Need talks only about the Taylor expansion for the approximation of transcendental functions:

The main application we want to express in this paper is the automatic (and configurable)
generation or Taylor approximation of usual transcendental functions such as exp or sin.

Taylor expansion relies on the smoothness of functions and their derivatives. Are you considering the floating point representation of real numbers as the discrete domain? Or, is this macro package doing something with finite differences to express function changes?

Back to the first line. What does it mean to "implement the concept of discrete ring"? Given by the user an addition and a multiplication operator, does it verify the ring or the field axioms like associativity, distribution of the multiplication over addition, existence of zero (and one) identity element(s), and inverses? What would happen if the user attempted to use operators that do not satisfy the corresponding axioms, for instance, using the semiring operators min(int32,int32) and plus(int32,int32) as the addition and multiplication?

Why is it advantageous to precompute at compile-time the addition and multiplication tables of a Galois field using macros instead of "normal" run-time codes? Why is it advantageous to have a macro to form continued fractions instead of a function at run time?

Some of the claims might also be incorrect. Why precomputing shrinks binary size? For example if I implement Horner's rule as a loop, and compare it against the code with the same loop unrolled, which code will have the smaller binary for a polynomial of degree 20?

I will reiterate that I do find this work interesting overall. However the article fails to provide a clear motivation why such a macro library is needed beyond the Taylor expansion of transcendental functions that allows the precomputation of specialized fast approximations.

[JeWaVe]

@editorialbot generate pdf

[editorialbot]

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

[JeWaVe]

Hi everyone and thanks for your comments.

I fixed documentation by adding actual examples and tried to rephrase the statement of need.

Basically the point is that aerobus provide both efficient polynomial evaluation and polynomial arithmetic at no runtime cost.

I hope it addresses your respective points.

Latest pdf above [EDIT : bibliography not updated by editorial bot] [[EDIT2 : I messed with references, should be OK]]

[JeWaVe]

@editorialbot generate pdf

[editorialbot]

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

[JeWaVe]

@editorialbot generate pdf

[editorialbot]

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

[JeWaVe]

One more comment if I may.

I rewrote my benchmarks to use google benchmarks but I wonder if I should include results in the paper, I mean they are OK but I usually don't trust benchmarks

[gkthiruvathukal]

@JeWaVe I am on travel but my short answer is to consider putting your results in a Figshare dataset (or similar) and consider linking your paper (or README page) to the dataset containing any current performance results. That way, you could update it it easily in the future without requiring changes to the JOSS paper itself.

[gkthiruvathukal]

@JeWaVe Let me know if you have any further questions so we can move to the next steps.

[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?