[REVIEW]: spaghetti: spatial network analysis in PySAL

[whedon]

Submitting author: @jGaboardi (James Gaboardi)
Repository: https://github.com/pysal/spaghetti
Version: v1.5.8
Editor: @usethedata
Reviewers: @martibosch, @usethedata
Archive: 10.5281/zenodo.4898079

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/52b8d0c81bbf311465b45bfc26379e74/status.svg)](https://joss.theoj.org/papers/52b8d0c81bbf311465b45bfc26379e74)

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.)

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Review checklist for @martibosch

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 (@jGaboardi) 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: Do the authors clearly state 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 @usethedata

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 (@jGaboardi) 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: Do the authors clearly state 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. @martibosch 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 😿

To fix this do the following two things:

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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]

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

OK DOIs

- 10.3390/ijgi4020815 is OK
- 10.1111/gean.12211 is OK
- 10.5281/zenodo.1343650 is OK
- 10.1111/j.0016-7363.2005.00674.x is OK
- 10.1002/9781119967101 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.5281/zenodo.3379659 is OK
- 10.5281/zenodo.3669853 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.5281/zenodo.1472807 is OK
- 10.1007/s11067-018-9427-9 is OK

MISSING DOIs

- 10.1007/978-3-642-03647-7_11 may be a valid DOI for title: PySAL: A Python Library of Spatial Analytical Methods

INVALID DOIs

- None

[usethedata]

Still working on getting the second reviewer. @martibosch -- you're free to go ahead with your review.

[whedon]

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

[usethedata]

@whedon generate pdf from branch joss

[whedon]

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

[whedon]

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

[jGaboardi]

@usethedata

• I am wondering if this is still on track or if there is anything I can do to assist?
• I am planning on doing a New Year release. Do I need to update anything here in the review once I do that?

[martibosch]

Hello all,

I am sorry for the delay in reviewing this submission. I am at the end of my thesis and this ended up buried in a pile of "TODOs". If this works for everybody, will review the submission by the end of this week. Or should I wait for the amendments that @jGaboardi is planning to include? How do we proceed regarding that, @usethedata?

Best,
Martí

[jGaboardi]

Or should I wait for the amendments that @jGaboardi is planning to include?

The release is a scheduled one to coincide with the biannual PySAL federation release. It will not include any change to the actual code-base or the text of the JOSS paper, just admin/maintenance adjustments for testing, docs, etc. I will get that out today, which will be v1.5.4 v1.5.6 (I had several hiccups correcting a bug in the release+publish workflow).

update: v1.5.6 is now a tagged release, and is available via pip and conda-forge.

[martibosch]

This would be all from my side. Looking forward to hear back from the authors. Let me clear out again that my intention is not to question the criteria of the authors (since they probably know better than me why they have made such choices), but rather ensure that the raised issues have been considered.

Best,
Martí

[jGaboardi]

Thanks for the thorough review, @martibosch. We will go through the issue you raised and respond ASAP.

@slumnitz @sjsrey

[usethedata]

@martibosch -- Thanks.
@jGaboardi -- My apologies for being missing in action on this. The last several weeks have been a bit challenging. I'll set the version on the software for the paper as one of the last things in the review process, so there aren't issues there. I'll work on the second reviewer shortly.

[arfon]

@jGaboardi – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[jGaboardi]

@arfon I have cut a fresh release and Zenodo archive with the following info. Let me know if I did this correctly.

title	spaghetti: spatial network analysis in PySAL
version	1.5.8
release	https://github.com/pysal/spaghetti/releases/tag/v1.5.8
doi	https://zenodo.org/record/4898079

@slumnitz @sjsrey looks like things are wrapping up here!

[arfon]

@whedon set 10.5281/zenodo.4898079 as archive

[whedon]

OK. 10.5281/zenodo.4898079 is the archive.

[arfon]

@whedon set v1.5.8 as version

[whedon]

OK. v1.5.8 is the version.

[arfon]

@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

- 10.3390/ijgi4020815 is OK
- 10.1111/gean.12211 is OK
- 10.5281/zenodo.1343650 is OK
- 10.1111/j.0016-7363.2005.00674.x is OK
- 10.1002/9781119967101 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.5281/zenodo.3379659 is OK
- 10.5281/zenodo.4569086 is OK
- 10.5281/zenodo.4572994 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.1472807 is OK
- 10.1007/s11067-018-9427-9 is OK
- 10.1002/9780470549094.ch5 is OK
- 10.21105/joss.01882 is OK
- 10.5281/zenodo.3265190 is OK

MISSING DOIs

- 10.1007/978-3-642-03647-7_11 may be a valid DOI for title: PySAL: A Python Library of Spatial Analytical Methods

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2357

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2357, 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]

@jGaboardi – please merge this PR which makes a small number of formatting fixes and removes a duplicate sentence pysal/spaghetti#626.

[jGaboardi]

@arfon pysal/spaghetti#626 is now merged.

[jGaboardi]

@whedon generate pdf

[whedon]

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

[arfon]

@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

- 10.3390/ijgi4020815 is OK
- 10.1111/gean.12211 is OK
- 10.5281/zenodo.1343650 is OK
- 10.1111/j.0016-7363.2005.00674.x is OK
- 10.1002/9781119967101 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.5281/zenodo.3379659 is OK
- 10.5281/zenodo.4569086 is OK
- 10.5281/zenodo.4572994 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.1472807 is OK
- 10.1007/s11067-018-9427-9 is OK
- 10.1002/9780470549094.ch5 is OK
- 10.21105/joss.01882 is OK
- 10.5281/zenodo.3265190 is OK

MISSING DOIs

- 10.1007/978-3-642-03647-7_11 may be a valid DOI for title: PySAL: A Python Library of Spatial Analytical Methods

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2358

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2358, 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.02826 joss-papers#2359
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02826
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]

@martibosch, @usethedata – many thanks for your reviews here and to @usethedata for editing too! JOSS relies upon the volunteer efforts of people like you and we simply wouldn't be able to do this without you ✨

On a personal note, thanks to @usethedata who is stepping down from the JOSS editorial team. Thanks Bruce for all of your help making JOSS the success it is 💖

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

[whedon]

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

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reStructuredText:
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