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

[editorialbot]

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

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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

@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

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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]

:wave: @openjournals/csism-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/5099, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@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]

@editorialbot generate pdf

[bonicim]

@danielskatz New DOI: 10.5281/zenodo.10795225

[editorialbot]

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

[danielskatz]

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]

@editorialbot set 10.5281/zenodo.10795225 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10795225

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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]

:wave: @openjournals/csism-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/5112, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[danielskatz]

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]

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5113
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06016
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...

[bpraggastis]

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