Submitting author: @SYalouz (SAAD YALOUZ) Repository: https://github.com/SYalouz/QuantNBody Branch with paper.md (empty if default branch): Version: v 1.0.0 Editor: @jarvist Reviewers: @wcwitt, @erikkjellgren 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

@wcwitt, 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 @jarvist 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 @wcwitt

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (401.0 files/s, 139888.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            993           1788           2346
Jupyter Notebook                 6              0           3738            958
TeX                              1             12              0            128
Markdown                         2             36              0             94
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            29           1042           5530           3544
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

Wordcount for paper.md is 1182

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

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

OK DOIs

- 10.21105/joss.00819 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- 10.21468/scipostphys.2.1.003 may be a valid DOI for title: QuSpin: a Python package for dynamics and exact diagonalisation of quantum many body systems part I: spin chains
- 10.21468/scipostphys.7.2.020 may be a valid DOI for title: QuSpin: a Python package for dynamics and exact diagonalisation of quantum many body systems. Part II: bosons, fermions and higher spins
- 10.22331/q-2020-10-11-341 may be a valid DOI for title: Yao. jl: Extensible, efficient framework for quantum algorithm design

INVALID DOIs

- None

Thanks @editorialbot !

OK, @SYalouz, there's some checking cross-references & augmenting your BibTeX suggestions above. You can re-regenerate the paper by asking Editorialbot here, once you've made changes to the repo.

You are welcome

Dear @jarvist,

As recommended, I have added the three missing DOIs in the bib file of the paper. I am going now to regenerate the paper.

@editorialbot generate pdf

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

@editorialbot add @erikkjellgren as reviewer

Many thanks to Erik @erikkjellgren for agreeing to review this paper! 🙌

@erikkjellgren added to the reviewers list!

@editorialbot check references

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

OK DOIs

- 10.21105/joss.00819 is OK
- 10.21468/SciPostPhys.7.2.020 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- 10.21468/scipostphys.2.1.003 may be a valid DOI for title: QuSpin: a Python package for dynamics and exact diagonalisation of quantum many body systems part I: spin chains
- 10.1088/2058-9565/ab8ebc may be a valid DOI for title: OpenFermion: the electronic structure package for quantum computers
- 10.22331/q-2020-10-11-341 may be a valid DOI for title: Yao. jl: Extensible, efficient framework for quantum algorithm design

INVALID DOIs

- None

Dear @jarvist,

Glad to see that a new reviewer has accepted to be part of the process.

I saw there were still some inconsistencies in the DOI sections of the .bib file. I went through all the references and added DOIs everywhere there was one missing. Hopefully, now there will not be problem on this side.

I am going to regenerate the pdf file and ask editorial bot for another round of reference checking. I take care of this.

@editorialbot generate pdf

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

@editorialbot check references

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

OK DOIs

- 10.1021/acs.jctc.7b00174 is OK
- 10.1063/5.0006074 is OK
- 10.21105/joss.00819 is OK
- 10.21468/scipostphys.2.1.003 is OK
- 10.21468/SciPostPhys.7.2.020 is OK
- 10.1088/2058-9565/ab8ebc is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2012.02.021 is OK
- 10.1016/j.cpc.2012.11.019 is OK
- 10.22331/q-2020-10-11-341 is OK

MISSING DOIs

- Errored finding suggestions for "Numba: A llvm-based python jit compiler", please try later

INVALID DOIs

- None

Review checklist for @wcwitt

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/SYalouz/QuantNBody?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@SYalouz) 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?

Review checklist for @erikkjellgren

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest 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 QuantNBody?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?

Dear @jarvist,

I contact you regarding citations to the package QuantNbody.

There are actually two papers from my group which have been realised using QuantNbody. One is already on arxiv, (see: https://arxiv.org/abs/2209.10302) and submitted to a journal, the second one will appear on arxiv by the end of the week (and submitted to a journal also this week).

I am wondering: May I inject explicit references to both these papers in the current manuscript ? This in order to demonstrate the interest of the package in current research projects.

Thanks in advance for your reply

Dear @jarvist ,

I come back to you to mention that the second paper from my group is now released on Arxiv (see https://arxiv.org/abs/2210.02325) where the package QuantNBody was employed. This paper has been submitted to a journal and it is now under review process.

I come back to you with the same questions as before: May I inject explicit references to both these papers in the current manuscript ? This in order to demonstrate the interest of the package in current research projects.

Thanks in advance for your reply

I see no problem with this, as long as there is a suitable scholarly discussion to put the citations in context. Certainly it's useful for a potential user of the package to see what can be achieved academically.

@erikkjellgren @wcwitt , how are your reviews coming along?

I will be done by the end of this week @jarvist

Ok, I have injected the two articles referencing the QuantNBody package, I will now generate the latest PDF version for the manuscript.

@editorialbot generate pdf

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

@editorialbot check references