[REVIEW]: VisWaterNet: A Python package for visualization of water distribution networks

[editorialbot]

Submitting author: @meghnathomas (Meghna Thomas)
Repository: https://github.com/tylertrimble/viswaternet
Branch with paper.md (empty if default branch):
Version: v1.1.0a
Editor: @crvernon
Reviewers: @erexer, @thurber
Archive: 10.5281/zenodo.7799929

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e9876602a7c3fdbfefe4ac8d913d3975"><img src="https://joss.theoj.org/papers/e9876602a7c3fdbfefe4ac8d913d3975/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e9876602a7c3fdbfefe4ac8d913d3975/status.svg)](https://joss.theoj.org/papers/e9876602a7c3fdbfefe4ac8d913d3975)

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

@erexer & @thurber, 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 @crvernon 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 @thurber

📝 Checklist for @erexer

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (568.7 files/s, 83049.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          27            827           1757           3533
reStructuredText                17            265            249            324
Jupyter Notebook                 1              0            557            125
make                             2             25              6             76
YAML                             3             11             15             64
TeX                              1              6              0             61
Markdown                         2             21              0             55
DOS Batch                        1              8              1             27
INI                              1              4              0             15
-------------------------------------------------------------------------------
SUM:                            55           1167           2585           4280
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 813

[editorialbot]

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

OK DOIs

- 10.1016/j.envsoft.2017.06.022 is OK
- 10.1101/gr.1239303 is OK
- 10.1007/978-3-642-18638-7_6 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1061/(ASCE)WR.1943-5452.0000191 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[thurber]

Review checklist for @thurber

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/tylertrimble/viswaternet?
• 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 (@meghnathomas) 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?

[crvernon]

👋 @meghnathomas, @erexer @thurber This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #5139 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[erexer]

Review checklist for @erexer

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/tylertrimble/viswaternet?
• 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 (@meghnathomas) 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?

[thurber]

I've started my review at tylertrimble/viswaternet#101

[erexer]

started my review at tylertrimble/viswaternet#111

[crvernon]

👋 @meghnathomas, @erexer, @thurber - It looks like you guys are making great progress. Please let me know if you have any questions!

[meghnathomas]

@crvernon thank you for checking in! We've made progress on the comments and I will formally reply to both reviews by tomorrow. I did have a question -- we've made several changes to the code so can we also release a new version on the repo and bump the PyPI version of our package? Or should we wait until the end of the review process?

[crvernon]

@meghnathomas you are good to release throughout the process as you normally would. I'll just take the final released version after all is done and ready to publish. Thanks!

[meghnathomas]

Perfect thank you for letting me know!

[erexer]

I've completed my review and approve the submission!

[crvernon]

📣 Mid-week Rally! 📣

It looks like @erexer and finished up their portion of the review and that @thurber and @meghnathomas are working well together to address additional items. Great progress so far and please let me know if you have any questions!

[thurber]

@editorialbot generate pdf

[editorialbot]

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

[thurber]

@editorialbot generate pdf

[editorialbot]

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

[thurber]

@crvernon, I have concluded my review and recommend the paper for acceptance!

[meghnathomas]

Hi @crvernon,

We have conducted a new Github release with tag v1.1.0a
We have archived the reviewed software in Zenodo and checked the metadata
This is the DOI of the archived version: 10.5281/zenodo.7799929

[crvernon]

@editorialbot set v1.1.0a as version

[editorialbot]

Done! version is now v1.1.0a

[crvernon]

@editorialbot set 10.5281/zenodo.7799929 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7799929

[crvernon]

@meghnathomas - thanks for putting together a really nice software product! Thanks to @erexer and @thurber for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@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

- 10.1016/j.envsoft.2017.06.022 is OK
- 10.1101/gr.1239303 is OK
- 10.1007/978-3-642-18638-7_6 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1061/(ASCE)WR.1943-5452.0000191 is OK
- 10.1016/j.envsoft.2018.05.016 is OK
- 10.5281/zenodo.831493 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/ese-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#4100, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[meghnathomas]

@crvernon @erexer @thurber thank you so much for your thoughtful feedback and very quick reviews! We appreciate that you made this such an easy process!

[kthyng]

For final checks I am doing the following:

• Check that version was updated
• Check that software archive exists, has been input to JOSS, and title and author list look good
• Check paper

[kthyng]

Those plots are so cool! Everything looks good so I am going to accept!

[kthyng]

@editorialbot accept

[editorialbot]

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

[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: Thomas
  given-names: Meghna
- family-names: Trimble
  given-names: Tyler
- family-names: Sela
  given-names: Lina
  orcid: "https://orcid.org/0000-0002-5834-8451"
contact:
- family-names: Thomas
  given-names: Meghna
doi: 10.5281/zenodo.7799929
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Thomas
    given-names: Meghna
  - family-names: Trimble
    given-names: Tyler
  - family-names: Sela
    given-names: Lina
    orcid: "https://orcid.org/0000-0002-5834-8451"
  date-published: 2023-04-11
  doi: 10.21105/joss.05139
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5139
  title: "VisWaterNet: A Python package for visualization of water
    distribution networks"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05139"
  volume: 8
title: "VisWaterNet: A Python package for visualization of water
  distribution 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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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 👉 Creating pull request for 10.21105.joss.05139 joss-papers#4110
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05139
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...

[kthyng]

Congrats on your new publication @meghnathomas! Many thanks to editor @crvernon and reviewers @erexer and @thurber for your time, hard work, and expertise!!

[editorialbot]

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

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.05139/status.svg)](https://doi.org/10.21105/joss.05139)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05139">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05139/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05139/status.svg
   :target: https://doi.org/10.21105/joss.05139

This is how it will look in your documentation:

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