[REVIEW]: spopt: a python package for solving spatial optimization problems in PySAL

[whedon]

Submitting author: @xf37 (Xin Feng)
Repository: https://github.com/pysal/spopt
Branch with paper.md (empty if default branch):
Version: 0.4.1
Editor: @vissarion
Reviewers: @tmickleydoyle, @apulverizer
Archive: 10.5281/zenodo.6638721

⚠️ 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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1413cf2c0cf3c561386949f2e1208563"><img src="https://joss.theoj.org/papers/1413cf2c0cf3c561386949f2e1208563/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1413cf2c0cf3c561386949f2e1208563/status.svg)](https://joss.theoj.org/papers/1413cf2c0cf3c561386949f2e1208563)

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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

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/pysal/spopt?
• 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 (@xf37) 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?

Review checklist for @tmickleydoyle

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 (@xf37) 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. @ArikaLZ, @samuel-rosa 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.

⭐ Important ⭐

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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (329.9 files/s, 125358.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              2              0             15           8419
Python                          29           1066           2633           2811
Jupyter Notebook                13              0           9542            641
YAML                            11              7             14            319
Markdown                         3             55              0            165
TeX                              2             20              2            157
CSS                              1             11              3             64
reStructuredText                 5             67             89             58
DOS Batch                        1              8              1             27
make                             1              6              6             16
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            69           1240          12305          12678
-------------------------------------------------------------------------------


Statistical information for the repository '6983c40ec08e3a4710e59e13' was
gathered on 2021/06/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
James Gaboardi                  35          1217            408            3.60
Pedro Camargo                    1             2              2            0.01
Serge                            1             7             14            0.05
Serge Rey                       23          2663            296            6.56
Xin Feng                        27         21564            353           48.61
eli knaap                        9            39          17963           39.93
rwei5                            6           304            254            1.24

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
James Gaboardi              934           76.7         11.3                4.60
Pedro Camargo                 2          100.0          0.0                0.00
Serge Rey                  2140           80.4          6.4                9.58
Xin Feng                   3384           15.7          6.0                7.03
eli knaap                    18           46.2          4.3               27.78
rwei5                        32           10.5         22.3               18.75

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1080/13658810600665111 may be a valid DOI for title: Efficient Regionalization Techniques for Socio-economic Geographical Units Using Minimum Spanning Trees
- 10.2307/1907301 may be a valid DOI for title: Optimum utilization of the transportation system
- 10.1016/j.omega.2019.102176 may be a valid DOI for title: Contemporary optimization application through geographic information systems
- 10.1080/13658816.2020.1759806 may be a valid DOI for title: Efficient Regionalization for Spatially Explicit Neighborhood Delineation
- 10.2307/622300 may be a valid DOI for title: A Geographical Solution to Scale and Aggregation Problems in Region-building, Partitioning and Spatial Modelling
- 10.1068/a270425 may be a valid DOI for title: Algorithms for Reengineering 1991 Census Geography
- 10.1007/978-3-642-03647-7_11 may be a valid DOI for title: PySAL: A Python library of spatial analytical methods
- 10.3390/ijgi4020815 may be a valid DOI for title: Open geospatial analytics with PySAL
- 10.31219/osf.io/yzt2p may be a valid DOI for title: Spatially-encouraged spectral clustering: a technique for blending map typologies and regionalization

INVALID DOIs

- https://doi.org/10.1111/j.1467-9787.2011.00743.x is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[vissarion]

Hi @xf37 it seems that several DOIs are missing from your submission and one is invalid as you can see above. Please fix this issue.

[whedon]

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

[whedon]

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

[samuel-rosa]

@whedon unfortunately I will not be able to conclude the review in due time. I have just been hit by a truckload of demands at my university. I hope that you find a suitable reviewer.

[whedon]

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

@whedon commands

[vissarion]

@whedon unfortunately I will not be able to conclude the review in due time. I have just been hit by a truckload of demands at my university. I hope that you find a suitable reviewer.

Hi @samuel-rosa that was an automated reminder from Joss robot (@whedon).

Just to be clear, if still interested in reviewing and you need more time to review this is totally understandable and we are very flexible especially during the codiv-19 era. On the other hand, if you decided that you cannot or do not want to review this is also understandable. Please let me know.

[jGaboardi]

@whedon generate pdf

[whedon]

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

[jGaboardi]

Hi @xf37 it seems that several DOIs are missing from your submission and one is invalid as you can see above. Please fix this issue.

We have fixed the issue with missing DOIs.

[vissarion]

Hi, @nickbearman, @ryankarlos, @ystouthart I think this submission matches your interests.

Would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[vissarion]

@whedon remove samuel-rosa as reviewer

[whedon]

OK, samuel-rosa is no longer a reviewer

[vissarion]

@whedon remove @samuel-rosa as reviewer

[editorialbot]

Done! Archive is now 10.5281/zenodo.6638721

[vissarion]

@editorialbot set 0.4.1 as version

[editorialbot]

Done! version is now 0.4.1

[vissarion]

@editorialbot generate pdf

[editorialbot]

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

[vissarion]

@jGaboardi hyperlinks do not work for me in general, unfortunately. In Ubuntu 12 with neither okular nor document viewer nor Firefox but Chrome opens them! Anyway maybe it is something local on my side or something with the markdown to pdf conversion. If this works for you I think I am OK.

[jGaboardi]

I can try to add in the links again and regenerate. If I do this though, will I have to bump to v0.4.2 and create a new release, etc.?

[tarleb]

@arfon: The GitHub Container Registry requires users to authenticate before pulling -- that would require some more changes to the action which I haven't implemented yet.

@jGaboardi: Can you try to enclose the links with </> as in <https://example.com>?

[jGaboardi]

@editorialbot generate pdf

[editorialbot]

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

[jGaboardi]

@vissarion OK, I regenerated the paper and can confirm that the link now open within Acrobat. I had only used Chrome before, but once I checked in Acrobat I can see that the previous versions' footnote links did not work. Should I cut a new spopt release and Zenodo Archive?

[martinfleis]

Should I cut a new spopt release and Zenodo Archive?

That shouldn't be necessary, I assume. There was no change to the package itself, only to the paper.

[vissarion]

Great, now hyperlinks work! Thanks @jGaboardi.
I also think the version and archive updates are not necessary.

[vissarion]

@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

- 10.1080/13658810600665111 is OK
- 10.1111/j.1467-9787.2011.00743.x is OK
- 10.2307/1907301 is OK
- 10.1145/321043.321046 is OK
- 10.1016/j.omega.2019.102176 is OK
- 10.1080/13658816.2020.1759806 is OK
- 10.2307/622300 is OK
- 10.1068/a270425 is OK
- 10.52324/001c.8285 is OK
- 10.3390/ijgi4020815 is OK
- 10.1111/gean.12276 is OK
- 10.31219/osf.io/yzt2p is OK
- 10.1287/opre.19.6.1363 is OK
- 10.1111/j.1435-5597.1974.tb00902.x is OK
- 10.1111/j.1538-4632.1970.tb00142.x is OK
- 10.1287/opre.12.3.450 is OK
- 10.5281/zenodo.4444156 is OK
- 10.1007/s12145-015-0221-7 is OK
- 10.1016/j.envsoft.2019.04.006 is OK
- 10.1007/s10109-021-00350-w is OK
- 10.1111/2041-210X.13478 is OK
- 10.1093/bioinformatics/btv562 is OK
- 10.32614/RJ-2018-063 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3276

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3276, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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.03330 joss-papers#3278
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03330
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]

@tmickleydoyle, @apulverize – many thanks for your reviews here and to @vissarion 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 ✨

@xf37 – your paper is now accepted and published in JOSS ⚡🚀💥

[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.03330/status.svg)](https://doi.org/10.21105/joss.03330)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03330">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03330/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03330/status.svg
   :target: https://doi.org/10.21105/joss.03330

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[tmickleydoyle]

w00t

[jGaboardi]

Thanks @tmickleydoyle & @apulverizer for the great reviews and @vissarion, @arfon, & @martinfleis for the editorial support!