[REVIEW]: Building, Importing, and Exporting GEXF Graph Files with rgexf

[whedon]

Submitting author: @gvegayon (George Vega Yon)
Repository: https://github.com/gvegayon/rgexf/
Version: v0.16.2
Editor: @fabian-s
Reviewer: @jonjoncardoso, @corneliusfritz
Archive: 10.5281/zenodo.5182709

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Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/369e7a58e1da094aee98c874c26e5f68"><img src="https://joss.theoj.org/papers/369e7a58e1da094aee98c874c26e5f68/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/369e7a58e1da094aee98c874c26e5f68/status.svg)](https://joss.theoj.org/papers/369e7a58e1da094aee98c874c26e5f68)

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@jonjoncardoso & @corneliusfritz, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @jonjoncardoso

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 repository url?
• 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 (@gvegayon) 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

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 #3520

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 and who the target audience is?
• 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?

Review checklist for @corneliusfritz

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 repository url?
• 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 (@gvegayon) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jonjoncardoso, @corneliusfritz it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (685.8 files/s, 117575.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              2              5              1           1896
R                               28            756           1189           1853
JavaScript                       5             90             96           1244
XML                              2              0              0            903
Markdown                         6            203              0            656
CSS                              2             71             15            198
TeX                              1             15              0            136
Python                           1             21              1            131
YAML                             5             35             14             89
Rmd                              2             46             90             65
HTML                             1              0              0             62
make                             2             14              0             36
Dockerfile                       1              4              0              8
-------------------------------------------------------------------------------
SUM:                            58           1260           1406           7277
-------------------------------------------------------------------------------


Statistical information for the repository 'eb6440f6130ddd1cf553f8e5' was
gathered on 2021/07/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
George G. Vega Yon               6          1802            535           86.85
George Vega Yon                  3           106             19            4.65
Joshua                           1           229              0            8.51

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
George G. Vega Yon         1583           87.8         27.1                6.19

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btq675 is OK
- 10.21105/joss.00814 is OK
- 10.1093/femsec/fiaa255 is OK
- 10.18637/jss.v093.i11 is OK
- 10.1038/nature23902 is OK
- 10.1038/nature25474 is OK
- 10.1038/s41598-018-24733-0 is OK
- 10.1109/WI.2016.0087 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[fabian-s]

thanks for agreeing to review this, @jonjoncardoso & @corneliusfritz!

[whedon]

👋 @corneliusfritz, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jonjoncardoso, please update us on how your review is going (this is an automated reminder).

[jonjoncardoso]

The only thing I missed was a CONTRIBUTING.md file or an equivalent section on the README to highlight how people could contribute to the code so as to adhere to the journal's documentation checklist:

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

Other than that, all good from my side. I've managed to install, follow the examples and generate some .gexf files myself.

I have used rgexf in the past for a netviz project and I remember it being very useful.

[corneliusfritz]

I also came to the same conclusion. There seem to be 16 open issues that are all not entirely solved, as far as I can see. I only have some minor additional remarks: Some tests/examples not nested in a demo, but the actual "Examples" Section would be helpful; also, the break commands should be placed so that each segment of code is one line to enable a faster learning curve and not necessitate scrolling through code all the time. Besides, the documentation of dynamic edges is not completely clear to me. For each edge, we need to provide some time where the edge starts and where it ends. Does the first column always need to be the time when it starts? If so, how are the examples interpreted, where the time indicated in the second row is before the time of the first row? And are the NAs marking some infinite end or beginning? Finally, what is the difference between a spell and an edge?

So far, I have always used CSV files to export my network data to Gephi, which works as well but going through the examples and trying out some things with my data, I believe that the package does some excellent and helpful work in that I will use it in future applications. In particular, the plot functionality is a nice add-on.

[fabian-s]

@gvegayon
could you give a brief update on your progress with the issues pointed out by the reviewers?

[gvegayon]

Hi! I think I have addressed all the comments. I am now working on the website, but installing the current version of the repo should work.

• I extended the documentation on spells and added a new example with it.
• I added some instructions on how to contribute, including a CODE_OF_CONDUCT.md file.
• Reorganized the breaks around the examples to make them easier to follow.
• I closed (and resolved) a few old issues. Only two regarding bugs are still open (which I will need to put more effort into solving.)

For convenience, you can see the changes made here.

[fabian-s]

@whedon generate pdf

[whedon]

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

[fabian-s]

@whedon check references

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btq675 is OK
- 10.21105/joss.00814 is OK
- 10.1093/femsec/fiaa255 is OK
- 10.18637/jss.v093.i11 is OK
- 10.1038/nature23902 is OK
- 10.1038/nature25474 is OK
- 10.1038/s41598-018-24733-0 is OK
- 10.1109/WI.2016.0087 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fabian-s]

@gvegayon congrats, looks like this is good to go -- to wrap it up please:

• 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.

[gvegayon]

• Tag: v0.16.2
• Zenodo archive: here
• Title matches paper (and right list of authors)
• DOI: 10.5281/zenodo.5182709

[fabian-s]

@whedon set 10.5281/zenodo.5182709 as archive

[whedon]

OK. 10.5281/zenodo.5182709 is the archive.

[fabian-s]

@whedon set v0.16.2 as version

[whedon]

OK. v0.16.2 is the version.

[fabian-s]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btq675 is OK
- 10.21105/joss.00814 is OK
- 10.1093/femsec/fiaa255 is OK
- 10.18637/jss.v093.i11 is OK
- 10.1038/nature23902 is OK
- 10.1038/nature25474 is OK
- 10.1038/s41598-018-24733-0 is OK
- 10.1109/WI.2016.0087 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2508

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2508, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.03456 joss-papers#2509
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03456
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...

[arfon]

@jonjoncardoso, @corneliusfritz – many thanks for your reviews here and to @fabian-s for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@gvegayon – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

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[gvegayon]

Hi! I just noticed that my last name is wrong in the citation. My last name is "Vega Yon," not Yon. This is not the first time this happens: #1427 (comment)

Last time it was a manual fix. Could you fix that? Thank you!

[kthyng]

@openjournals/dev Could someone do a manual name fix on a published paper (see note above)? Thanks!