Joss-reviews: [REVIEW]: textnets: A Python package for text analysis with networks

[whedon]

Submitting author: @jboynyc (John Boy)
Repository: https://github.com/jboynyc/textnets
Version: v0.4.10
Editor: @gkthiruvathukal
Reviewer: @sara-02, @tresoldi
Archive: 10.5281/zenodo.4028610

:warning: JOSS reduced service mode :warning:

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.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/827fa29da12bd11fe1841f8135f5b840/status.svg)](https://joss.theoj.org/papers/827fa29da12bd11fe1841f8135f5b840)

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

@sara-02 & @tresoldi, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @gkthiruvathukal 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 ✨

Review checklist for @sara-02

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@jboynyc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @tresoldi

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@jboynyc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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. @sara-02, @tresoldi it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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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To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2594 with the following error:

Can't find any papers to compile :-(

[jboynyc]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[tresoldi]

@jboynyc great library, thank you! I can see myself using it for at least one project I have in mind.

Nothing to mention in terms of the code and package structure, quality is very good both in terms of coding and documenting. I've just filed an issue on the only real problem I saw. Some additional points/comments here:

• Given your audience, it might be valid to offer the library as a conda package as well
• As a suggestion, I'd list all dependencies in separate requirements(-x).txt files, to be read inside setup.py. I know some people prefer to keep an internal list, so no real issue here.

On the manuscript:

• I am afraid I have to ask for a better introduction to the library in the "Background" section. There currently is no clear-cut statement of need, and while the advantages offered by the library are evident for people from the field, those might be opaque for the "diverse, non-specialist audience" we aim. This is particularly clear when you mention the "novel way of analysis" without giving an example of non-novel, common-place ways. The manuscript would improve with a short, clear statement of need ("The library addresses X", "The library is needed in order to X") and, if possible, with a comparison with simpler ways of document clustering in the documentation. A simpler comparison of networks commonly found in the literature and those produced by textnets could be enough.
• I also had problems with figure placing in JOSS in the past, but could you try to have more text in the first page?

[jboynyc]

Thanks, @tresoldi! I will push a new version of the paper by the end of the week adding a more detailed statement of need to the background section and doing my best to fix figure placement. I'll let you know when I'm ready.

I also really like your idea of creating a Conda package. I've started looking into it.

[jboynyc]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[tresoldi]

All my points were addressed, only issue https://github.com/jboynyc/textnets/issues/14 still pending.

[jboynyc]

Release 0.4.10 closes jboynyc/textnets#14.

Many thanks @tresoldi for the helpful and encouraging review!

[tresoldi]

Great, @jboynyc , and thanks once more for this package.

@gkthiruvathukal No further requests from me, approved.

[jboynyc]

Great, @jboynyc , and thanks once more for this package.

I'd love to hear about any projects you use it for, so please do ping me!

[jboynyc]

I made a minor update to the paper noting the ability to install from conda-forge.

[jboynyc]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[gkthiruvathukal]

@sara-02 and @tresoldi, it looks like we are mostly good to go on this submission. Can you let us know if there are any other issues and check all remaining boxes in your review checklist as appropriate?

Then we can move toward acceptance.

[tresoldi]

@gkthiruvathukal We can move towards acceptance, for me. All boxes checked. :smiley:

[sara-02]

@jboynyc I have a query regarding this point

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

I could not find a command for the same, have added an issue here: https://github.com/jboynyc/textnets

Apart from this point, the rest of the checklist is complete from my side as well.

[sara-02]

The above query has been sorted.

[sara-02]

@gkthiruvathukal I have completed my checklist as well.
We are good to move forward.

[jboynyc]

Thanks for your careful review, @sara-02! :+1:

[gkthiruvathukal]

@tresoldi and @sara-02. Thanks for your help on this review! We appreciate all of the help from our reviewers during what remains a challenging time for the world.

@jboynyc Thanks for your work to address all input. Please do the following:

• [x] Make a tagged release of your software, and list the version tag of the archived version here.
• [x] Archive the reviewed software in Zenodo
• [x] Check the Zenodo deposit 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.
• [x] List the Zenodo DOI of the archived version here.

[jboynyc]

• Latest tagged release is 0.4.10
• Zenodo DOI for that release is 10.5281/zenodo.4028610

[gkthiruvathukal]

@whedon set v0.4.10 as versino

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[gkthiruvathukal]

@whedon set v0.4.10 as version

[whedon]

OK. v0.4.10 is the version.

[gkthiruvathukal]

@whedon set 10.5281/zenodo.4028610 as archive

[whedon]

OK. 10.5281/zenodo.4028610 is the archive.

[gkthiruvathukal]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #2594 with the following error:

Can't find any papers to compile :-(

[gkthiruvathukal]

@whedon generate pdf from joss-submission

[whedon]

PDF failed to compile for issue #2594 with the following error:

Can't find any papers to compile :-(

[gkthiruvathukal]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[danielskatz]

@gkthiruvathukal - when the paper is in a branch, you need to accept it from the branch:

[danielskatz]

@whedon accept from branch joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1812

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1812, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true from branch joss

[whedon]

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

OK DOIs

- 10.1146/annurev-soc-081715-074206 is OK
- 10.1073/pnas.1607151113 is OK
- 10.5281/zenodo.1469356 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.1126/sciadv.aaq1360 is OK
- 10.1111/jtsb.12086 is OK
- 10.21105/joss.00774 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

👋 @sara-02 - above you say that the unchecked item in your list is satisfied, so I am going to move the acceptance forward, but if you could check off the item itself, it will be slightly cleaner.

[danielskatz]

👋 @jboynyc - Some fixes are needed in the paper: https://github.com/jboynyc/textnets/pull/19 and https://github.com/jboynyc/textnets/pull/20

[sara-02]

wave @sara-02 - above you say that the unchecked item in your list is satisfied, so I am going to move the acceptance forward, but if you could check off the item itself, it will be slightly cleaner.

Done

[jboynyc]

wave @jboynyc - Some fixes are needed in the paper: jboynyc/textnets#19 and jboynyc/textnets#20

Merged! Thanks for catching those.

[danielskatz]

@whedon accept from branch joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1146/annurev-soc-081715-074206 is OK
- 10.1073/pnas.1607151113 is OK
- 10.5281/zenodo.1469356 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.1126/sciadv.aaq1360 is OK
- 10.1111/jtsb.12086 is OK
- 10.21105/joss.00774 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1815

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1815, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true from branch joss

[danielskatz]

@whedon accept deposit=true from branch joss

[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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1816
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02594
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @jboynyc (John Boy)!!

And thanks to @sara-02 & @tresoldi for reviewing, and @gkthiruvathukal for editing!

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02594/status.svg)](https://doi.org/10.21105/joss.02594)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02594">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02594/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02594/status.svg
   :target: https://doi.org/10.21105/joss.02594

This is how it will look in your documentation:

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[jboynyc]

Thanks to all involved!