[REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #6016

editorialbot · 2023-11-03T10:43:10Z

Submitting author: @brendapraggastis (Brenda Praggastis)
Repository: https://github.com/pnnl/HyperNetX
Branch with paper.md (empty if default branch): paper
Version: v2.2.0p
Editor: @danielskatz
Reviewers: @szhorvat, @IvanIsCoding, @drj11
Archive: 10.5281/zenodo.10795225

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f"><img src="https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f/status.svg)](https://joss.theoj.org/papers/97a1ebb3cfc47070c672cb5e6f2c474f)

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

@szhorvat & @IvanIsCoding, 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 @danielskatz 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 @szhorvat

📝 Checklist for @drj11

📝 Checklist for @IvanIsCoding

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-11-03T10:43:14Z

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

editorialbot · 2023-11-03T10:43:25Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.53 s (189.1 files/s, 428840.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          48           2280           5245           5609
Jupyter Notebook                12              0         211574           1108
reStructuredText                21            389            358            818
Markdown                         6            204              0            554
DOS Batch                        1             34              2            227
TeX                              1             23              0            206
YAML                             6             37             29            178
make                             2             34             22             67
INI                              2              4              2             35
TOML                             2              0              0             27
-------------------------------------------------------------------------------
SUM:                           101           3005         217232           8829
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-03T10:43:26Z

Wordcount for paper.md is 1206

editorialbot · 2023-11-03T10:43:35Z

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

OK DOIs

- 10.1007/978-3-030-48478-1_1 is OK
- 10.3390/math10050759 is OK
- 10.1109/hipc53243.2021.00045 is OK
- 10.1109/tvcg.2022.3153895 is OK
- 10.1140/epjds/s13688-020-00231-0 is OK
- 10.1371/journal.pcbi.1011190 is OK
- 10.1016/s0924-6509(09)x7013-3 is OK
- 10.1016/s0924-6509(08)x7007-2 is OK
- 10.1186/s12859-021-04197-2 is OK
- 10.48550/arXiv.2208.03103 is OK
- 10.1093/comnet/cnad019 is OK
- 10.48550/arXiv.2208.06894 is OK
- 10.1007/978-3-030-67318-5_25 is OK
- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1007/978-3-030-25070-6_9 is OK
- 10.1101/2023.09.29.560191 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-03T10:45:18Z

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

danielskatz · 2023-11-03T10:46:12Z

@szhorvat, @IvanIsCoding, and @drj11 - Thanks for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6016 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

danielskatz · 2023-11-03T11:29:57Z

@editorialbot add @drj11 as reviewer

editorialbot · 2023-11-03T11:30:00Z

@drj11 added to the reviewers list!

drj11 · 2023-11-03T11:39:17Z

Review checklist for @drj11

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/pnnl/HyperNetX?
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 (@brendapraggastis) 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?

szhorvat · 2023-11-03T12:21:52Z

Review checklist for @szhorvat

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/pnnl/HyperNetX?
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 (@brendapraggastis) made major contributions to the software? Does the full list of paper authors seem appropriate and complete? See [REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #6016 (comment)
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 See [joss] Contributor guide should be more specific, and probably shouldn't suggest Rust as the language pnnl/HyperNetX#144

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? See [REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #6016 (comment)
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?

IvanIsCoding · 2023-11-03T22:10:35Z

Review checklist for @IvanIsCoding

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/pnnl/HyperNetX?
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 (@brendapraggastis) 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?

IvanIsCoding · 2023-11-15T04:40:47Z

I have reviewed the software package and preliminarily I believe it would be a great addition to the papers published at the Journal.

Software

With regards to the software, I do not have objections. I believe HyperNetX is a significant scholarly contribution and that it is as mature as if not more mature than other packages published in this journal.

From a Software Engineering point of view, I also found the that the test suite of the package meets the standards for publication. I was able to install the software and run the tests without issues. I was also able to generate a code coverage report. There are some warnings when running the tests and the coverage for the Drawing module is on the lower side. But overall the software is tested and Continuous Integration is in place to detect regressions, which is nice.

Documentation

For the documentation I focused more on the provided Jupyter Notebooks and A Gentle Introduction to Hypergraph Mathematics provided in the docs. There are also documentations for every function and class, but I admit I haven't scrutinized each method and looked at the greater picture.

As a reviewer with a greater emphasis on graphs than hypegraphs, I found that the "gentle" introduction answered most of the questions for the statement of need and defined the terminology for the package.

The Jupyter Notebooks available in Colab were also a pleasant surprise. I think they exemplify how to use the package and highlight the visualization features that come with HyperNetX.

Paper

This is the only section where I think there is feedback to give to the authors from my side. Namely:

The "HNX-Widget: Interactive Diagrams of Hypergraphs" is my least favourite section of the paper. I do not believe it aggregates much given the word limit recommended by JOSS. I suggest using an image with a detailed caption to convey the message better
The authors should cite pandas following the guidelines of the package
The authors should cite NetworkX following the guidelines of the package

danielskatz · 2023-11-21T18:41:28Z

👋 @brendapraggastis - while two reviews are currently in progress, you could respond to (or act on) @IvanIsCoding's comments and issue during this time.

brendapraggastis · 2023-11-21T19:56:16Z

Thanks @IvanIsCoding and @danielskatz . We are addressing your comments and should be able to push paper changes in the next week or so.

szhorvat · 2023-11-21T19:58:14Z

Sorry about the long absence. If all goes according to plan I hope to finish the review by Dec 14.

brendapraggastis · 2023-11-22T00:37:21Z

@IvanIsCoding Thanks for the detailed review. I've incorporated your suggesttions in the paper in https://github.com/pnnl/HyperNetX/tree/paper/HNX_Paper.

danielskatz · 2023-11-22T01:13:50Z

@editorialbot generate pdf

@brendapraggastis - you could issue this command too, if you make further changes. I'll also check the references again next. Commands need to be the first thing in a comment

danielskatz · 2023-11-22T01:13:59Z

@editorialbot check references

editorialbot · 2023-11-22T01:14:24Z

⚠️ An error happened when generating the pdf. Problem with ORCID (0000-0000-0000-0000) for Sinan Aksoy. Invalid ORCID.

editorialbot · 2023-11-22T01:14:30Z

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

OK DOIs

- 10.1007/978-3-030-48478-1_1 is OK
- 10.3390/math10050759 is OK
- 10.1109/hipc53243.2021.00045 is OK
- 10.1109/tvcg.2022.3153895 is OK
- 10.1140/epjds/s13688-020-00231-0 is OK
- 10.1371/journal.pcbi.1011190 is OK
- 10.1016/s0924-6509(09)x7013-3 is OK
- 10.1016/s0924-6509(08)x7007-2 is OK
- 10.1186/s12859-021-04197-2 is OK
- 10.48550/arXiv.2208.03103 is OK
- 10.1093/comnet/cnad019 is OK
- 10.48550/arXiv.2208.06894 is OK
- 10.1007/978-3-030-67318-5_25 is OK
- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1007/978-3-030-25070-6_9 is OK
- 10.1101/2023.09.29.560191 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz · 2023-11-22T01:14:59Z

@brendapraggastis - if an author has an ORCID, please enter it. If not, please remove the line about it.

brendapraggastis · 2023-11-22T17:26:47Z

@editorialbot generate pdf

bonicim · 2024-03-06T22:10:00Z

Software has been stored on Zenodo at https://zenodo.org/records/10790797

DOI: 10.5281/zenodo.10790797

danielskatz · 2024-03-07T07:56:34Z

@editorialbot set 10.5281/zenodo.10790797 as archive

editorialbot · 2024-03-07T07:56:36Z

Done! archive is now 10.5281/zenodo.10790797

danielskatz · 2024-03-07T07:57:01Z

@editorialbot recommend-accept

editorialbot · 2024-03-07T07:57:03Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-07T07:57:40Z

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

OK DOIs

- 10.1007/978-3-030-48478-1_1 is OK
- 10.3390/math10050759 is OK
- 10.1109/hipc53243.2021.00045 is OK
- 10.1109/tvcg.2022.3153895 is OK
- 10.1140/epjds/s13688-020-00231-0 is OK
- 10.1371/journal.pcbi.1011190 is OK
- 10.1016/s0924-6509(09)x7013-3 is OK
- 10.1016/s0924-6509(08)x7007-2 is OK
- 10.1186/s12859-021-04197-2 is OK
- 10.48550/arXiv.2208.03103 is OK
- 10.1093/comnet/cnad019 is OK
- 10.48550/arXiv.2208.06894 is OK
- 10.1007/978-3-030-67318-5_25 is OK
- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1007/978-3-030-25070-6_9 is OK
- 10.1101/2023.09.29.560191 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- No DOI given, and none found for title: The Stanford GraphBase: a platform for combinatori...
- No DOI given, and none found for title: igraph enables fast and robust network analysis ac...
- No DOI given, and none found for title: The igraph software package for complex network re...
- No DOI given, and none found for title: HyperThesis: Topological Hypothesis Management in ...
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...

INVALID DOIs

- None

editorialbot · 2024-03-07T07:58:27Z

👋 @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#5099, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-03-07T08:06:43Z

@brendapraggastis, @bonicim - sorry, but I see two small changes needed in the paper that were in my PR but didn't make it into the changes you made. Please add a space in this line

In its latest release, HNX 2.0 uses Pandas dataframes[@reback2020pandas;@mckinney-proc-scipy-2010] as its underlying data structure,

so that it becomes

In its latest release, HNX 2.0 uses Pandas dataframes [@reback2020pandas;@mckinney-proc-scipy-2010] as its underlying data structure,

And similarly, in

a statistics package as well as a full suite of hypergraph analysis and visualization tools[@landry2023].

so that it becomes

a statistics package as well as a full suite of hypergraph analysis and visualization tools [@landry2023].

bonicim · 2024-03-07T20:19:40Z

@editorialbot generate pdf

bonicim · 2024-03-07T20:20:37Z

@danielskatz New DOI: 10.5281/zenodo.10795225

editorialbot · 2024-03-07T20:20:55Z

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

danielskatz · 2024-03-09T21:25:19Z

Thanks @bonicim - we actually don't need the paper in the archive, so you didn't need to create a new archive or tag, just to update the .md file. However, I didn't say this clearly. In any case, I'll check again now.

danielskatz · 2024-03-09T21:25:40Z

@editorialbot set 10.5281/zenodo.10795225 as archive

editorialbot · 2024-03-09T21:25:43Z

Done! archive is now 10.5281/zenodo.10795225

danielskatz · 2024-03-09T21:25:52Z

@editorialbot recommend-accept

editorialbot · 2024-03-09T21:25:54Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-09T21:26:27Z

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

OK DOIs

- 10.1007/978-3-030-48478-1_1 is OK
- 10.3390/math10050759 is OK
- 10.1109/hipc53243.2021.00045 is OK
- 10.1109/tvcg.2022.3153895 is OK
- 10.1140/epjds/s13688-020-00231-0 is OK
- 10.1371/journal.pcbi.1011190 is OK
- 10.1016/s0924-6509(09)x7013-3 is OK
- 10.1016/s0924-6509(08)x7007-2 is OK
- 10.1186/s12859-021-04197-2 is OK
- 10.48550/arXiv.2208.03103 is OK
- 10.1093/comnet/cnad019 is OK
- 10.48550/arXiv.2208.06894 is OK
- 10.1007/978-3-030-67318-5_25 is OK
- 10.1137/20M1355896 is OK
- 10.1007/978-3-030-71704-9_1 is OK
- 10.21105/joss.05162 is OK
- 10.1007/978-3-030-25070-6_9 is OK
- 10.1101/2023.09.29.560191 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- No DOI given, and none found for title: The Stanford GraphBase: a platform for combinatori...
- No DOI given, and none found for title: igraph enables fast and robust network analysis ac...
- No DOI given, and none found for title: The igraph software package for complex network re...
- No DOI given, and none found for title: HyperThesis: Topological Hypothesis Management in ...
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...

INVALID DOIs

- None

editorialbot · 2024-03-09T21:27:39Z

👋 @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#5112, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-03-09T21:36:13Z

@editorialbot accept

editorialbot · 2024-03-09T21:36:15Z

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

danielskatz · 2024-03-09T21:43:18Z

Congratulations to @brendapraggastis (Brenda Praggastis) and @bonicim and co-authors on your publication!!

And thanks to @szhorvat, @IvanIsCoding, and @drj11 for reviewing!
JOSS depends on volunteers and we couldn't do this without you

editorialbot · 2024-03-09T21:43:21Z

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: Praggastis
  given-names: Brenda
  orcid: "https://orcid.org/0000-0003-1344-0497"
- family-names: Aksoy
  given-names: Sinan
  orcid: "https://orcid.org/0000-0002-3466-3334"
- family-names: Arendt
  given-names: Dustin
  orcid: "https://orcid.org/0000-0003-2466-199X"
- family-names: Bonicillo
  given-names: Mark
  orcid: "https://orcid.org/0009-0003-9764-2180"
- family-names: Joslyn
  given-names: Cliff
  orcid: "https://orcid.org/0000-0002-5923-5547"
- family-names: Purvine
  given-names: Emilie
  orcid: "https://orcid.org/0000-0003-2069-5594"
- family-names: Shapiro
  given-names: Madelyn
  orcid: "https://orcid.org/0000-0002-2786-7056"
- family-names: Yun
  given-names: Ji Young
doi: 10.5281/zenodo.10795225
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Praggastis
    given-names: Brenda
    orcid: "https://orcid.org/0000-0003-1344-0497"
  - family-names: Aksoy
    given-names: Sinan
    orcid: "https://orcid.org/0000-0002-3466-3334"
  - family-names: Arendt
    given-names: Dustin
    orcid: "https://orcid.org/0000-0003-2466-199X"
  - family-names: Bonicillo
    given-names: Mark
    orcid: "https://orcid.org/0009-0003-9764-2180"
  - family-names: Joslyn
    given-names: Cliff
    orcid: "https://orcid.org/0000-0002-5923-5547"
  - family-names: Purvine
    given-names: Emilie
    orcid: "https://orcid.org/0000-0003-2069-5594"
  - family-names: Shapiro
    given-names: Madelyn
    orcid: "https://orcid.org/0000-0002-2786-7056"
  - family-names: Yun
    given-names: Ji Young
  date-published: 2024-03-09
  doi: 10.21105/joss.06016
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6016
  title: "HyperNetX: A Python package for modeling complex network data
    as hypergraphs"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06016"
  volume: 9
title: "HyperNetX: A Python package for modeling complex network data as
  hypergraphs"

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 · 2024-03-09T21:43:25Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-09T21:43:26Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06016 joss-papers#5113
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06016
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

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bpraggastis · 2024-03-11T01:37:28Z

Thanks for getting us through the process! @danielskatz @szhorvat @drj11 @IvanIsCoding and of course Mark @bonicim .

editorialbot added Makefile Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Nov 3, 2023

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editorialbot mentioned this issue Nov 3, 2023

[PRE REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #5955

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IvanIsCoding mentioned this issue Nov 15, 2023

[joss] Improve class signatures in documentation pnnl/HyperNetX#126

Open

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 7, 2024

danielskatz closed this as completed Mar 9, 2024

editorialbot added accepted published Papers published in JOSS labels Mar 9, 2024

editorialbot mentioned this issue Sep 22, 2024

[PRE REVIEW]: PANINIpy: Package of Algorithms for Nonparametric Inference with Networks in Python #7263

Closed

[REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #6016

[REVIEW]: HyperNetX: A Python package for modeling complex network data as hypergraphs #6016

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