[REVIEW]: XGI: A Python package for higher-order interaction networks about joss-reviews HOT 65 CLOSED

Just a quick note that we renamed our organization to be more concise, so now the repo is located at https://github.com/xgi-org/xgi in case the prior link stops working.

from joss-reviews.

Thanks for the ping @vissarion and sorry for the delay!

I have finished the review and this paper should definitely be included in JOSS! The paper is well written and the package and documentation covers all the necessary details. There could be a some more information about things like "How to contribute", as currently it still leaves a lot to the reader. But I think this is good to go :) We (NetworkX) have also been thinking about how to interact with HyperGraphs in the future so this was a fun read!

from joss-reviews.

Thanks for the submission. I have already found the software to be quite useful. The paper is, in my opinion, concise and well-written. The documentation and tests are in quite a good shape, especially considering that the project is in heavy, active development by multiple contributors. I congratulate the team and wholeheartedly recommend the publication of the paper.

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@vissarion Will be able to finish up shortly, maybe in the next few days. Apologies for the delay, I had wrapped up another JOSS review and then things got quite busy.

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That should be fine, thanks.

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@tbsexton I have removed you from reviewers to continue with this submission in a timely manner. Thanks for your time spend in this submission.

@MridulS @arashbm Thank you for your reviews!

@nwlandry When a submission is ready to be accepted, we ask that the authors to issue a new tagged release of the software (if changed), and archive it (see this guide). Please do this and post the version number and archive DOI in this thread.

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Thanks @vissarion, references should be all fixed now.

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@danielskatz I hopefully addressed the ambiguity of the first sentence and I merged in your PR fixing the references. Let me know if there is anything else I can provide. Thanks so much!

from joss-reviews.

Congratulations to @nwlandry (Nicholas Landry) and co-authors!!

And thanks to @arashbm and @MridulS for reviewing, and to @vissarion for editing!
We couldn't do this without your voluntary efforts

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (751.3 files/s, 177404.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             3              1              0           9920
Python                          64           2929           5117           7480
Jupyter Notebook                12              0           4851            869
Markdown                         8            232              0            577
reStructuredText                50            375            563            303
TeX                              1             23              0            235
DOS Batch                        1             34              2            227
SVG                              1              1              1            173
make                             1             33              8            159
YAML                             2             16             16             81
INI                              1              0              0              7
CSS                              1              0              0              5
-------------------------------------------------------------------------------
SUM:                           145           3644          10558          20036
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1025

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

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

OK DOIs

- 10.48550/arXiv.2208.00909 is OK
- 10.1038/s42005-022-00963-7 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.1016/j.physrep.2020.05.004 is OK
- 10.1137/18M1203031 is OK
- 10.1093/comnet/cnaa018 is OK
- 10.1093/bioinformatics/btac347 is OK
- 10.1137/21M1399427 is OK
- 10.1038/s41467-019-10431-6 is OK
- 10.1103/PhysRevResearch.2.033410 is OK
- 10.1103/PhysRevLett.124.218301 is OK
- 10.1103/PhysRevE.101.032310 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.122.248301 is OK
- 10.24166/im.01.2020 is OK
- 10.48550/arXiv.2203.03060 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Review checklist for @arashbm

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/ComplexGroupInteractions/xgi?
• 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 (@nwlandry) 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?

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Review checklist for @tbsexton

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/ComplexGroupInteractions/xgi?
• 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 (@nwlandry) 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?

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Review checklist for @MridulS

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/ComplexGroupInteractions/xgi?
• 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 (@nwlandry) 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?

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Hi, @tbsexton @MridulS any news from your reviews?

from joss-reviews.

@tbsexton we now have 2 positive reviews. I generally want to wait for your review too but if this is an issue we can move forward without it. What do you think?

Is it possible that you will have your review ready in the next, say 2-3, days?

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@editorialbot remove @tbsexton from reviewers

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@tbsexton removed from the reviewers list!

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@editorialbot generate pdf

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

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@editorialbot check references

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

OK DOIs

- 10.48550/arXiv.2208.00909 is OK
- 10.1038/s42005-022-00963-7 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.1016/j.physrep.2020.05.004 is OK
- 10.1137/18M1203031 is OK
- 10.1093/comnet/cnaa018 is OK
- 10.1093/bioinformatics/btac347 is OK
- 10.1137/21M1399427 is OK
- 10.1038/s41467-019-10431-6 is OK
- 10.1103/PhysRevResearch.2.033410 is OK
- 10.1103/PhysRevLett.124.218301 is OK
- 10.1103/PhysRevE.101.032310 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.122.248301 is OK
- 10.24166/im.01.2020 is OK
- 10.48550/arXiv.2203.03060 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

Thank you very much @vissarion and all three reviewers for your time.

I've updated two references from their arXiv version to their published one just now.

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@editorialbot generate pdf

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

from joss-reviews.

@editorialbot generate pdf

from joss-reviews.

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

from joss-reviews.

@editorialbot generate pdf

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

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@editorialbot check references

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

OK DOIs

- 10.1063/5.0116747 is OK
- 10.1038/s42005-022-00963-7 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.1016/j.physrep.2020.05.004 is OK
- 10.1137/18M1203031 is OK
- 10.1093/comnet/cnaa018 is OK
- 10.1093/bioinformatics/btac347 is OK
- 10.1137/21M1399427 is OK
- 10.1038/s41467-019-10431-6 is OK
- 10.1103/PhysRevResearch.2.033410 is OK
- 10.1103/PhysRevLett.124.218301 is OK
- 10.1103/PhysRevE.101.032310 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.122.248301 is OK
- 10.24166/im.01.2020 is OK
- 10.1038/s41467-023-37190-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

from joss-reviews.

Hi @vissarion! Thanks so much! I have released XGI 0.6 on PyPI and have made an associated DOI: https://doi.org/10.5281/zenodo.7939055 - let me know if there's anything else I can provide.

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@editorialbot set 10.5281/zenodo.7939055 as archive

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Done! archive is now 10.5281/zenodo.7939055

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@editorialbot set v0.6 as version

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Done! version is now v0.6

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@editorialbot generate pdf

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

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Thanks @nwlandry for the info. I created an issue related to paper references.

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@editorialbot generate pdf

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

from joss-reviews.

@editorialbot generate pdf

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

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1063/5.0116747 is OK
- 10.1038/s42005-022-00963-7 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.1016/j.physrep.2020.05.004 is OK
- 10.1137/18M1203031 is OK
- 10.1093/comnet/cnaa018 is OK
- 10.1093/bioinformatics/btac347 is OK
- 10.1137/21M1399427 is OK
- 10.1038/s41467-019-10431-6 is OK
- 10.1103/PhysRevResearch.2.033410 is OK
- 10.1103/PhysRevLett.124.218301 is OK
- 10.1103/PhysRevE.101.032310 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.122.248301 is OK
- 10.24166/im.01.2020 is OK
- 10.1038/s41467-023-37190-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4240, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

from joss-reviews.

👋 @nwlandry - I'm the track editor, finishing the processing for this submission. I've found some minor issues in the bib, as shown in xgi-org/xgi#364 - please merge this, or let me know what you disagree with.

In addition, I wonder if "which model" in the first sentence of the paper should be "which models"? I can't tell if this refers to the networks or the library, so both could be correct.

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I will think of how to re-write the first sentence. Thanks for noticing.

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1063/5.0116747 is OK
- 10.1038/s42005-022-00963-7 is OK
- 10.1016/j.softx.2022.101301 is OK
- 10.1016/j.physrep.2020.05.004 is OK
- 10.1137/18M1203031 is OK
- 10.1093/comnet/cnaa018 is OK
- 10.1093/bioinformatics/btac347 is OK
- 10.1137/21M1399427 is OK
- 10.1038/s41467-019-10431-6 is OK
- 10.1103/PhysRevResearch.2.033410 is OK
- 10.1103/PhysRevLett.124.218301 is OK
- 10.1103/PhysRevE.101.032310 is OK
- 10.6084/m9.figshare.1164194 is OK
- 10.1103/PhysRevLett.122.248301 is OK
- 10.24166/im.01.2020 is OK
- 10.1038/s41467-023-37190-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4241, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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@editorialbot accept

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

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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:

cff-version: "1.2.0"
authors:
- email: [email protected]
  family-names: Landry
  given-names: Nicholas W.
  orcid: "https://orcid.org/0000-0003-1270-4980"
- family-names: Lucas
  given-names: Maxime
  orcid: "https://orcid.org/0000-0001-8087-2981"
- family-names: Iacopini
  given-names: Iacopo
  orcid: "https://orcid.org/0000-0001-8794-6410"
- family-names: Petri
  given-names: Giovanni
  orcid: "https://orcid.org/0000-0003-1847-5031"
- family-names: Schwarze
  given-names: Alice
  orcid: "https://orcid.org/0000-0002-9146-8068"
- family-names: Patania
  given-names: Alice
  orcid: "https://orcid.org/0000-0002-3047-4376"
- family-names: Torres
  given-names: Leo
  orcid: "https://orcid.org/0000-0002-2675-2775"
contact:
- email: [email protected]
  family-names: Landry
  given-names: Nicholas W.
  orcid: "https://orcid.org/0000-0003-1270-4980"
doi: 10.5281/zenodo.7939055
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - email: [email protected]
    family-names: Landry
    given-names: Nicholas W.
    orcid: "https://orcid.org/0000-0003-1270-4980"
  - family-names: Lucas
    given-names: Maxime
    orcid: "https://orcid.org/0000-0001-8087-2981"
  - family-names: Iacopini
    given-names: Iacopo
    orcid: "https://orcid.org/0000-0001-8794-6410"
  - family-names: Petri
    given-names: Giovanni
    orcid: "https://orcid.org/0000-0003-1847-5031"
  - family-names: Schwarze
    given-names: Alice
    orcid: "https://orcid.org/0000-0002-9146-8068"
  - family-names: Patania
    given-names: Alice
    orcid: "https://orcid.org/0000-0002-3047-4376"
  - family-names: Torres
    given-names: Leo
    orcid: "https://orcid.org/0000-0002-2675-2775"
  date-published: 2023-05-17
  doi: 10.21105/joss.05162
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5162
  title: "XGI: A Python package for higher-order interaction networks"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05162"
  volume: 8
title: "XGI: A Python package for higher-order interaction networks"

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.

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#4242
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05162
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

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Great, thank you! This closes #5162

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@danielskatz, I checked the tagged pull request and PDF and everything looks great. Good to close this issue now. Thanks!

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05162/status.svg)](https://doi.org/10.21105/joss.05162)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05162">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05162/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05162/status.svg
   :target: https://doi.org/10.21105/joss.05162

This is how it will look in your documentation:

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