[REVIEW]: pymnet: A Python Library for Multilayer Networks #6930

editorialbot · 2024-06-26T18:00:21Z

Submitting author: @ercco (Tarmo Nurmi)
Repository: https://github.com/mnets/pymnet
Branch with paper.md (empty if default branch): publication
Version: v1.0.0
Editor: @danielskatz
Reviewers: @ClaudMor, @pitmonticone, @nwlandry
Archive: 10.5281/zenodo.12806499

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/db2862edc9b952d110f791d1559d7e93/status.svg)](https://joss.theoj.org/papers/db2862edc9b952d110f791d1559d7e93)

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

@ClaudMor & @pitmonticone & @nwlandry, 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 @pitmonticone

📝 Checklist for @nwlandry

📝 Checklist for @ClaudMor

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

editorialbot · 2024-06-26T18:00:24Z

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:

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

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editorialbot · 2024-06-26T18:00:38Z

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

OK DOIs

- 10.1093/comnet/cnu016 is OK
- 10.1109/TNSE.2017.2753963 is OK
- 10.1093/comnet/cnac005 is OK
- 10.48550/arXiv.2308.00083 is OK
- 10.1007/978-3-642-19754-3_16 is OK
- 10.1137/1.9781611972870.13 is OK
- 10.1038/srep04547 is OK
- 10.1109/TEM.2020.3032160 is OK
- 10.1007/s41109-020-00301-2 is OK
- 10.1088/1367-2630/17/7/073029 is OK
- 10.7554/eLife.43094 is OK
- 10.1093/scan/nsaa069 is OK
- 10.1007/s41109-021-00429-9 is OK
- 10.21105/joss.05116 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-06-26T18:00:50Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (673.1 files/s, 167182.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          45           2305           3040           9324
reStructuredText                 9            209            131            320
TeX                              1             14              0            147
make                             1             28              6            143
Markdown                         2             37              0            101
HTML                             1             41              0             99
YAML                             4             25             10             92
TOML                             1              6              0             54
INI                              1              0              0             12
-------------------------------------------------------------------------------
SUM:                            65           2665           3187          10292
-------------------------------------------------------------------------------

Commit count by author:

   252	Mikko Kivelä
   150	Tarmo Nurmi
    21	dataspider
    14	Arash Badie-Modiri
     3	Kivelä Mikko
     2	Corinna Coupette
     2	Luiz Irber
     1	DaminK
     1	Pietro Monticone
     1	alexguirre
     1	sala515

editorialbot · 2024-06-26T18:00:54Z

Paper file info:

📄 Wordcount for paper.md is 1215

✅ The paper includes a Statement of need section

editorialbot · 2024-06-26T18:00:56Z

License info:

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

editorialbot · 2024-06-26T18:01:34Z

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

danielskatz · 2024-06-26T18:01:40Z

👋 @ClaudMor, @pitmonticone, and @nwlandry - 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#6930 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 2-4 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.

nwlandry · 2024-06-26T18:09:13Z

Review checklist for @nwlandry

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/mnets/pymnet?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ercco) 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?

Additional comments:

This is an excellent software product. It's clear that some major thought went into this package and I think that it's a tremendous contribution to the field. For this reason, I added a few issues which are non-essential (I mentioned this in those particular issues) but will improve the package in years to come. Great work.

pitmonticone · 2024-06-28T15:46:37Z

Review checklist for @pitmonticone

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/mnets/pymnet?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ercco) 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?

ClaudMor · 2024-06-28T17:55:47Z

Review checklist for @ClaudMor

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/mnets/pymnet?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@ercco) 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?

pitmonticone · 2024-06-28T18:11:36Z

Review Issues

ClaudMor · 2024-06-29T23:08:13Z

Review Issues

danielskatz · 2024-07-01T13:10:18Z

thanks @pitmonticone and @ClaudMor for getting started quickly. I see some progress on at least some of the issues already too, so thanks to @ercco and @dataspider

pitmonticone · 2024-07-01T20:48:22Z

I have a question for @danielskatz.

In one of the final sections of the paper, the authors cite several scientific publications (e.g., kivela2014, cozzo2015structure, kivela2017) as examples of projects that have adopted the open-source software package ⁠ pymnet ⁠. However, the first commit in the ⁠ pymnet ⁠ GitHub repository is dated October 2020. This suggests that the software was not publicly available as an open-source package, or even as supplementary code, at the time those earlier publications were written.

How does JOSS handle citations of projects that purportedly used code before it was publicly available as an open-source package?

Specifically:

⁠Should the authors provide additional context or evidence to clarify how the software was accessed and used in these earlier works?
⁠⁠Is there a requirement for the authors to disclose whether an earlier, non-public version of the software was used by these cited projects?

Your guidance on addressing this issue would be greatly appreciated, as I am not at all sure how to evaluate this.

Thank you in advance for your assistance.

danielskatz · 2024-07-01T20:59:38Z

@pitmonticone - I don't see an issue here. The paper is about the software, and projects that have used it are just statement about those projects seeing some value in it. The license and status of the software at that time probably doesn't have anything to do with the value projects saw in using it. You can ask the authors about this, if you want, but I personally don't think the how they accessed it is necessary to add in the paper. JOSS certainly doesn't have any policies on this.

pitmonticone · 2024-07-01T21:01:41Z

Ok, thank you very much for the clarification @danielskatz.

arashbm · 2024-07-02T04:46:20Z

@pitmonticone The first commit is actually from 2013. The original software was mainly available on BitBucket up until some years ago, after which it was moved to GitHub.

pitmonticone · 2024-07-02T05:40:12Z

Thank you very much, @arashbm, for the reference. I reviewed the GitHub commit history from browser but wasn't able to locate it.

ercco · 2024-07-02T09:06:08Z

@editorialbot generate pdf

editorialbot · 2024-07-02T09:07:15Z

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

ercco · 2024-07-02T09:26:06Z

@danielskatz According to this reviewer comment: mnets/pymnet#24, we have updated the paper title to one suggested by the reviewer (pymnet: A Python Library for Multilayer Networks). However, the titles of the submission and this review issue, etc. are unchanged. I didn't find any method of editing the title post-submission on the JOSS submission page. I suppose we finish the review under the old title, and for the actual publication, the title can be updated to match the new paper title?

danielskatz · 2024-07-23T00:03:54Z

👋 @ercco - my suggested changes are in mnets/pymnet#51 Please merge this, or let me know what you disagree with, then we can proceed.

ercco · 2024-07-23T14:19:40Z

@danielskatz - I have now merged the suggested changes!

danielskatz · 2024-07-23T14:20:31Z

@editorialbot generate pdf

editorialbot · 2024-07-23T14:22:14Z

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

danielskatz · 2024-07-23T14:23:31Z

@ercco - please check this PDF to make sure everything looks ok, including the changes. If so, then:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
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.
Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

ercco · 2024-07-24T10:50:46Z

@editorialbot generate pdf

editorialbot · 2024-07-24T10:52:04Z

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

ercco · 2024-07-24T10:59:48Z

The figure placement was a bit awkward in the article pdf, leading to large white spaces at the bottom of pages 2 and 3. I moved and scaled figure 1 slightly to make the layout better.

danielskatz · 2024-07-24T12:22:14Z

@ercco - that's fine, this looks better.

I'll continue to await your actions on the bullets above.

ercco · 2024-07-24T15:13:47Z

@danielskatz Here are the archived and tagged versions of pymnet - we bumped the version number to 1.0.0:

Zenodo DOI: https://doi.org/10.5281/zenodo.12806499
Tagged release on GitHub: https://github.com/mnets/pymnet/releases/tag/v1.0.0
PyPI release of v1.0.0: https://pypi.org/project/pymnet/1.0.0/

danielskatz · 2024-07-24T15:18:29Z

@editorialbot set 10.5281/zenodo.12806499 as archive

editorialbot · 2024-07-24T15:18:32Z

Done! archive is now 10.5281/zenodo.12806499

danielskatz · 2024-07-24T15:18:38Z

@editorialbot set v1.0.0 as version

editorialbot · 2024-07-24T15:18:40Z

Done! version is now v1.0.0

danielskatz · 2024-07-24T15:18:48Z

@editorialbot recommend-accept

editorialbot · 2024-07-24T15:18:50Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-07-24T15:19:05Z

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

OK DOIs

- 10.1093/comnet/cnu016 is OK
- 10.1109/TNSE.2017.2753963 is OK
- 10.1093/comnet/cnac005 is OK
- 10.48550/arXiv.2308.00083 is OK
- 10.1007/978-3-642-19754-3_16 is OK
- 10.1137/1.9781611972870.13 is OK
- 10.1038/srep04547 is OK
- 10.1109/TEM.2020.3032160 is OK
- 10.1007/s41109-020-00301-2 is OK
- 10.1088/1367-2630/17/7/073029 is OK
- 10.7554/eLife.43094 is OK
- 10.1093/scan/nsaa069 is OK
- 10.1007/s41109-021-00429-9 is OK
- 10.21105/joss.05116 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-07-24T15:20:43Z

👋 @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#5668, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-07-24T15:38:53Z

@editorialbot accept

editorialbot · 2024-07-24T15:38:56Z

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

editorialbot · 2024-07-24T15:45:45Z

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: Nurmi
  given-names: Tarmo
  orcid: "https://orcid.org/0000-0003-0258-7776"
- family-names: Badie-Modiri
  given-names: Arash
  orcid: "https://orcid.org/0000-0002-2027-360X"
- family-names: Coupette
  given-names: Corinna
  orcid: "https://orcid.org/0000-0001-9151-2092"
- family-names: Kivelä
  given-names: Mikko
  orcid: "https://orcid.org/0000-0003-2049-1954"
doi: 10.5281/zenodo.12806499
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Nurmi
    given-names: Tarmo
    orcid: "https://orcid.org/0000-0003-0258-7776"
  - family-names: Badie-Modiri
    given-names: Arash
    orcid: "https://orcid.org/0000-0002-2027-360X"
  - family-names: Coupette
    given-names: Corinna
    orcid: "https://orcid.org/0000-0001-9151-2092"
  - family-names: Kivelä
    given-names: Mikko
    orcid: "https://orcid.org/0000-0003-2049-1954"
  date-published: 2024-07-24
  doi: 10.21105/joss.06930
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6930
  title: "pymnet: A Python Library for Multilayer Networks"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06930"
  volume: 9
title: "pymnet: A Python Library for Multilayer 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.

editorialbot · 2024-07-24T15:45:49Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-07-24T15:45:49Z

🚨🚨🚨 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.06930 joss-papers#5669
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06930
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2024-07-24T15:53:37Z

Congratulations to @ercco (Tarmo Nurmi) and co-authors on your publication!!

And thanks to @ClaudMor, @pitmonticone and @nwlandry for reviewing!
JOSS depends on volunteers and wouldn't be successful without your work

editorialbot · 2024-07-24T15:53:39Z

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

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.06930/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06930/status.svg
   :target: https://doi.org/10.21105/joss.06930

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ercco · 2024-07-25T10:01:16Z

On behalf of all of us, a huge thank you to @ClaudMor, @pitmonticone, @nwlandry, and @danielskatz! All of your comments and suggestions really made the library and the paper much better, thank you for your work. This was a very smooth process overall.

editorialbot added HTML Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Jun 26, 2024

editorialbot assigned danielskatz Jun 26, 2024

editorialbot mentioned this issue Jun 26, 2024

[PRE REVIEW]: pymnet: A Multilayer-Networks Library for Python #6901

Closed

This was referenced Jul 2, 2024

[REVIEW]: Use black and isort to format mnets/pymnet#34

Closed

[REVIEW] Add to multilayer introduction and make it more visible. mnets/pymnet#36

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 24, 2024

editorialbot added accepted published Papers published in JOSS labels Jul 24, 2024

danielskatz closed this as completed Jul 24, 2024

[REVIEW]: pymnet: A Python Library for Multilayer Networks #6930

[REVIEW]: pymnet: A Python Library for Multilayer Networks #6930

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