editorialbot commented 4 months ago

Submitting author: !--author-handle-->@thraraujo@phibeck<!--end-editor-- Reviewers: @eliotwrobson, @AnnikaStein Archive: 10.5281/zenodo.11214737

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f395fc3a9e1d482af1e0fc0d1eb17d2e"><img src="https://joss.theoj.org/papers/f395fc3a9e1d482af1e0fc0d1eb17d2e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f395fc3a9e1d482af1e0fc0d1eb17d2e/status.svg)](https://joss.theoj.org/papers/f395fc3a9e1d482af1e0fc0d1eb17d2e)

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

@eliotwrobson & @AnnikaStein, 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 @phibeck 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 @AnnikaStein

📝 Checklist for @eliotwrobson

editorialbot commented 4 months ago

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editorialbot commented 4 months ago

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

OK DOIs

- 10.48550/arXiv.0909.2331 is OK
- 10.1093/oso/9780198534891.001.0001 is OK
- 10.1007/978-1-4612-0979-9 is OK
- 10.1017/CBO9780511535024 is OK
- 10.1017/CBO9780511628832 is OK
- 10.1093/acprof:oso/9780198568490.001.0001 is OK
- 10.48550/arXiv.1110.6703 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (1470.3 files/s, 269525.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            50           1607            150          10380
SVG                              3              0              0           2689
CSS                              6            223             57           1014
JavaScript                      12            131            221            880
Python                          22            411            422            800
Markdown                         5             77              0            382
TeX                              2             73             10            368
Jupyter Notebook                10              0           3371            277
reStructuredText                17            124            214            172
YAML                             2              7             12             51
DOS Batch                        1              8              1             26
TOML                             1              4              0             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           132           2669           4465          17064
-------------------------------------------------------------------------------

Commit count by author:

    38  thraraujo
     5  Thiago Araujo

editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 531

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 4 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

AnnikaStein commented 4 months ago

Review checklist for @AnnikaStein

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/thraraujo/pysymmpol?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@thraraujo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution. -> Technically, there is a list of dependencies, but I believe it is rather strict (exactly one python version, tested with exact versions of numpy / sympy). Could this not be relaxed to be more inclusive? Like python 3.9 upwards or anything like that, same for the packages in question. For the record, I tested with python 3.11 instead of 3.12 and what I tested so far works fine.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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 -> Here I believe, given that it's generated with a tool, this could be improved to be closer to the actual community. For example, there is nodejs, npm etc mentioned - however, the package is pure python, no web frontend development involved. Probably this should instead include means to find out the version of python or packages that might influence the behavior of pysymmpol. So what actually needs to be known in advance to contribute.

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

thraraujo commented 4 months ago

Hi @AnnikaStein, thanks. I will work on these things in the next few days. Talk soon.

eliotwrobson commented 4 months ago

Review checklist for @eliotwrobson

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/thraraujo/pysymmpol?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@thraraujo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

General Comments

I haven't looked at the paper in detail yet, but I will start by opening a few issues on the repo for some things I noticed in the code. I'm going to be using this book to get some background on symmetric polynomials, (there is also this other book). It may be a good idea to cite these as newer, accessible introductions to this topic.

thraraujo commented 4 months ago

Hi @eliotwrobson,

I'll address the last issue here as it's pertinent to concerns raised by @AnnikaStein. It's worth noting that both @phibeck and @AnnikaStein are fellow physicists.

Regarding your comment:

One of the review checklist items is a discussion of the "state of the field" about other software packages. Some discussion of this would be very useful, even if it is just stating what operations are supported by this package that do not exist elsewhere (i.e. not in sympy).

I've incorporated another section on the state of the field, delineating the main disparities between our package and SageMath. Additionally, I've included insights on the target audience.

Regarding your comment:

The section on the core features of the package would be much stronger if there were an example of the analysis that could be done with the package in relation to the discussion of CFTs. As someone with a pure combinatorics background, it's a little hard to tell what types of analysis can be done with the package in the context of theoretical physics.

Describing the types of analyses possible isn't straightforward, given the myriad combinatorial problems in physics. However, I've appended references to Okounkov's and Marino's papers, which align with my interests. In any case, you might check examples ranging from condensed matter physics Zinn-Justin to string theory Nekrasov-Okounkov.
One relevant example within your interests is in representation theory. Quantum mechanics operators (representing measurable objects) are unitary (Lie groups SU(n)), and through the Schur-Weyl duality, their representations are labeled by Young diagrams, related to symmetric group representations. Schur polynomials serve as characters in these representations.
While I refrain from self-citation, I've conducted research leveraging this software to examine objects called tau functions, as elaborated in this paper. These objects were expanded in terms of Schur and Hall-Littlewood polynomials.
Lastly, I aim to keep the paper concise, adhering to <700 words, as per @phibeck's comments.

thraraujo commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

eliotwrobson commented 4 months ago

@thraraujo your changes look good! The main item from the review checklist was the discussion of the state of other packages, and that section is clear. I'll go ahead and close the issue and check that item off of my list 👍🏽

thraraujo commented 4 months ago

Hi @eliotwrobson and @AnnikaStein, thanks for all the comments.

Hi @phibeck, the only missing point appears to be the Summary in @AnnikaStein's checklist. @eliotwrobson's checklist agrees that the summary already provides a high-level description understandable even to non-specialists. In my opinion, key terms like Manipulation, Polynomials, and Symmetric are very precise, so I don't want to give an additional high-level description of the types of manipulations or symmetric polynomials the package deals with. Since this is a minor point, I'll leave the decision to you.

AnnikaStein commented 4 months ago

Sorry @thraraujo for not being clear on what I meant with this point - I was a bit hesitant to check it as the summary contains abbreviations, "AdS/CFT" which, in my opinion, a "diverse, non-specialist audience" would likely not understand without further reading. For someone with a physics background, one may always infer that field theories are meant when you see the letters FT next to each other :), but if one looks at it from a different perspective, it's a non-trivial set of abbreviations.

thraraujo commented 4 months ago

Hi @AnnikaStein, actually, it is a fair take, and I'd missed it. Now it's fixed. Thanks

thraraujo commented 3 months ago

Dear @phibeck , it appears that the reviewers have completed their evaluations; and I am awaiting your decision or further instructions. Could you please provide an update on the next steps in the process? Best

phibeck commented 3 months ago

Hi @thraraujo thanks for checking in. I'm travelling this week but will look into it tomorrow. I believe we are ready to proceed, but let me get back to you tomorrow.

phibeck commented 3 months ago

Thank you very much for an incredibly speedy and thorough review, @AnnikaStein and @eliotwrobson! :rocket: And thank you @thraraujo for addressing all comments timely and adequately. :raised_hands: This is by far the fastest review I have seen so far, thank you all! :1st_place_medal:

@thraraujo the reviewers have recommended the submission for publication. There are a few more steps before we finalize the publication. At this point could you please:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

phibeck commented 3 months ago

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

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

phibeck commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

OK DOIs

- 10.48550/arXiv.0909.2331 is OK
- 10.1093/oso/9780198534891.001.0001 is OK
- 10.1007/978-1-4612-0979-9 is OK
- 10.1017/CBO9780511535024 is OK
- 10.1017/CBO9780511628832 is OK
- 10.1093/acprof:oso/9780198568490.001.0001 is OK
- 10.48550/arXiv.1110.6703 is OK
- 10.5281/zenodo.593563 is OK
- 10.1142/9789812704016_0037 is OK

MISSING DOIs

- None

INVALID DOIs

- None

phibeck commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

thraraujo commented 3 months ago

Hi @phibeck , thanks

Thank you very much for an incredibly speedy and thorough review, @AnnikaStein and @eliotwrobson! 🚀 And thank you @thraraujo for addressing all comments timely and adequately. 🙌 This is by far the fastest review I have seen so far, thank you all! 🥇

Kudos to @AnnikaStein and @eliotwrobson! They were indeed very fast, and I sincerely believe the package is much better now.

[X] Make a tagged release of your software, and list the version tag of the archived version here.

I have already done this, version v0.1.2

[X] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

Archived here: https://zenodo.org/records/11214737

[X] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

Done.

[X] Please list the DOI of the archived version here.

DOI: 10.5281/zenodo.11214737

thraraujo commented 3 months ago

Hi @phibeck, any news?!?

phibeck commented 3 months ago

@editorialbot set v0.1.2 as version

editorialbot commented 3 months ago

Done! version is now v0.1.2

phibeck commented 3 months ago

@editorialbot set 10.5281/zenodo.11214737 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.11214737

phibeck commented 3 months ago

@thraraujo thanks for the reminder. I'm away for a workshop since last week so response is a bit slow. Here are a few more comments/suggestions for the manuscript. Please have a look when you have a moment.

line 20f: I assume the four references are associated with the four fields mentioned here, but the association is a bit ambiguous. Could you place the reference directly with the mentioned field?
line 36: CFT is already defined in line 14, so I think it's not necessary here
line 36f: when citing multiple references at once, citing them as Blah blah [@doe99; @smith2000; @smith2004] should render them as one block (see https://pandoc.org/MANUAL.html#extension-citations)
line 37: "for examples of physical problems..."
line 78: Hall capitalized
line 80: Simons capitalized

thraraujo commented 3 months ago

Hi @phibeck, it's done. Thanks.

phibeck commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

OK DOIs

- 10.48550/arXiv.0909.2331 is OK
- 10.1093/oso/9780198534891.001.0001 is OK
- 10.1007/978-1-4612-0979-9 is OK
- 10.1017/CBO9780511535024 is OK
- 10.1017/CBO9780511628832 is OK
- 10.1093/acprof:oso/9780198568490.001.0001 is OK
- 10.48550/arXiv.1110.6703 is OK
- 10.5281/zenodo.593563 is OK
- 10.1142/9789812704016_0037 is OK

MISSING DOIs

- None

INVALID DOIs

- None

phibeck commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

phibeck commented 3 months ago

:wave: @thraraujo looks good, thank you. I'll hand this over to the Track Editor-in-chief!

phibeck commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.48550/arXiv.0909.2331 is OK
- 10.1093/oso/9780198534891.001.0001 is OK
- 10.1007/978-1-4612-0979-9 is OK
- 10.1017/CBO9780511535024 is OK
- 10.1017/CBO9780511628832 is OK
- 10.1093/acprof:oso/9780198568490.001.0001 is OK
- 10.48550/arXiv.1110.6703 is OK
- 10.5281/zenodo.593563 is OK
- 10.1142/9789812704016_0037 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/pe-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5409, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

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

editorialbot commented 3 months ago

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: Araujo given-names: Thiago orcid: "https://orcid.org/0000-0001-5792-2530" doi: 10.5281/zenodo.11214737 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Araujo given-names: Thiago orcid: "https://orcid.org/0000-0001-5792-2530" date-published: 2024-05-30 doi: 10.21105/joss.06724 issn: 2475-9066 issue: 97 journal: Journal of Open Source Software publisher: name: Open Journals start: 6724 title: PySymmPol - Symmetric Polynomials type: article url: "https://joss.theoj.org/papers/10.21105/joss.06724" volume: 9 title: PySymmPol - Symmetric Polynomials ```

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 commented 3 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5413
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06724
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 3 months ago

Congratulations @thraraujo on your article's publication in JOSS! Please consider signing up as a reviewer if you haven't already.

Many thanks to @eliotwrobson and @AnnikaStein for reviewing this, and @phibeck for editing.

editorialbot commented 3 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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reStructuredText:
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   :target: https://doi.org/10.21105/joss.06724

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openjournals / joss-reviews

[REVIEW]: pySymmPol: Symmetric Polynomials #6724

Status

Reviewer instructions & questions

Checklists

Review checklist for @AnnikaStein

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @eliotwrobson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

General Comments

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance