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[REVIEW]: splot: visual analytics for spatial statistics #1882

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whedon opened this issue Nov 11, 2019 · 56 comments
Closed

[REVIEW]: splot: visual analytics for spatial statistics #1882

whedon opened this issue Nov 11, 2019 · 56 comments

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@whedon
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@whedon whedon commented Nov 11, 2019

Submitting author: @slumnitz (Stefanie Lumnitz)
Repository: https://github.com/pysal/splot
Version: v1.1.1
Editor: @leouieda
Reviewer: @ResidentMario, @martinfleis
Archive: 10.5281/zenodo.3724199

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/59166a5cec24d54bafec741aa08c3ba8"><img src="https://joss.theoj.org/papers/59166a5cec24d54bafec741aa08c3ba8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/59166a5cec24d54bafec741aa08c3ba8/status.svg)](https://joss.theoj.org/papers/59166a5cec24d54bafec741aa08c3ba8)

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

@ResidentMario & @martinfleis, 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 @leouieda know.

Please try and complete your review in the next two weeks

Review checklist for @ResidentMario

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

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 (@slumnitz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @martinfleis

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

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 (@slumnitz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?
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@whedon whedon commented Nov 11, 2019

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

⭐️ 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:

watching

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

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
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@whedon whedon commented Nov 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 11, 2019

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@leouieda leouieda commented Nov 11, 2019

👋 @slumnitz @ResidentMario, @martinfleis this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread 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 openjournals/joss-reviews#1882 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 reviews to be completed within about 4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me here (@leouieda) or email me privately if you have any questions/concerns.

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@martinfleis martinfleis commented Nov 17, 2019

Hi,

I would like to close up my review. Majority of splot's feature is currently focused on visualising the data from various PySAL sub-modules, which is extremely helpful in understanding their outputs. However, splot goes further than that (and has plans to do even more). A prime example is Value-by-alpha plotting feature. The default visual style of splot is very polished, and I would also say that there is no need to touch the defaults and plots can go directly to publications. That is not very common for scientific software.

During my review, I have opened a couple of issues (all linked above). Most of them are just recommendations, rather than critical issues. Before I tick Installation box, I would like to see pysal/splot#88 fixed as there are currently two versions of instructions, with those in the documentation failing. The second issue I would like to see resolved to tick the final box is pysal/splot#92, but that seems to be just a syntax issue.

To sum it up, splot is a valuable part of Python geospatial world and I will be watching closely its future development. My last recommendation is to have a detailed discussion with geoplot (already started in pysal/splot#21) to agree on the scope of both projects and avoid duplication of effort in the future.

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@ResidentMario ResidentMario commented Nov 19, 2019

I'm done with my review. I don't have any hard blocking issues to add to those opened by @martinfleis.

But I will say that I have some qualms with the uneven documentation in splot. For example, one of the three tutorial notebooks, titled Exploratory Analysis of Spatial Data, mentions the following statistical concepts without giving much explanation or linking the user to a reference on what these things are: Moran's I, local Moran, Donatns [sic?] variable, bivariate Moran statistic. Furthermore, the tutorials only cover a small subset of the library functions: there are many plotters documented at some length in the API Reference which do not appear in the any of the tutorials.

I do not think this is a blocking issue because the documentation is still within the acceptable range for JOSS (all of the relevant methods are covered by the API Reference, which doesn't leave any fields unexplained and is generally very well-packed with example images), but I feel that it's a definite area for improvement for the package as a whole.

I have left more general feedback about documentation with the broader PySAL team in the PySAL Gitter chat.

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@leouieda leouieda commented Nov 25, 2019

Hi @martinfleis @ResidentMario thank you for your reviews! 🎉

@ResidentMario that is a good point about the tutorial coverage and I agree that it's not a requirement for JOSS to have full coverage of tutorials. However, the citation/linking of statistical concepts is highly encouraged as I see scientific software documentation (particularly for JOSS) as a major part of the scholarship. @slumnitz could you please go through the tutorials and add references as you see necessary?

@martinfleis @slumnitz please let me know when the install and figure caption issues are resolved.

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@slumnitz slumnitz commented Nov 28, 2019

@martinfleis @ResidentMario @leouieda thank you for your thorough review, comments and great suggestions! I will implement them in the next couple of weeks or as soon as I can and let you know when everything is done.

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@danielskatz danielskatz commented Jan 7, 2020

@slumnitz - any news on this?

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@slumnitz slumnitz commented Jan 7, 2020

@slumnitz - any news on this?

@danielskatz I will start working on it slowly again now. It got a bit delayed due to snowmageddon and a couple of electricity outages here in BC, Canada, which are expected to ease in the next wo weeks.

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@leouieda leouieda commented Jan 8, 2020

@slumnitz thank you for the update 👍 Please keep us informed of your progress.

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@slumnitz slumnitz commented Jan 21, 2020

@martinfleis @ResidentMario and @leouieda thank you for your review and comments. The new splot release includes solutions to the major documentation issues outlined. Currently as you noticed, splot tutorials require previous knowledge in spatial statistical analysis and are not aimed to teach statistical concepts.

Do you think a new tutorial like a beginners guide to spatial statistical analysis in splot would be suitable to fill this gap, or would you recommend referencing great blogposts, statistical literature is enough?

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@martinfleis martinfleis commented Jan 22, 2020

@whedon generate pdf

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@whedon whedon commented Jan 22, 2020

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@martinfleis martinfleis commented Jan 22, 2020

@slumnitz the figure captions formatting is still strange. JOSS has its own style for captions, see the last published paper. Your figures seems to be encapsulated in links, which are not working anyway, causing captions not to render.

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@martinfleis martinfleis commented Jan 22, 2020

@slumnitz to answer your question, I think good links are enough.

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@leouieda leouieda commented Jan 30, 2020

@slumnitz thank you keeping us in the loop. As @martinfleis said, the figures weren't rendering properly. I submitted a PR fixing this.

Also, we now have a compilation service that you can use to preview the paper (even on branches before merging PRs): https://whedon.theoj.org

@ResidentMario I see you still have the "Installation" review item unchecked. Could you please see if this has been addressed in the new version of splot?

@martinfleis you have the "Quality of writing" item unchecked. Has this been addressed in the updated paper?

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@martinfleis martinfleis commented Jan 30, 2020

@leouieda I kept it unchecked due to figures formatting issue. Your PR resolves it, but note that you made a PR to your forked repo not the original repo.

I'll take it as resolved and finish my review.

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@whedon whedon commented Mar 23, 2020

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

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@arfon arfon commented Mar 23, 2020

@whedon set 10.5281/zenodo.3724199 as archive

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@whedon whedon commented Mar 23, 2020

OK. 10.5281/zenodo.3724199 is the archive.

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@arfon arfon commented Mar 23, 2020

@whedon generate pdf

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@whedon whedon commented Mar 23, 2020

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@arfon arfon commented Mar 23, 2020

@whedon accept

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@whedon whedon commented Mar 23, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Mar 23, 2020

PDF failed to compile for issue #1882 with the following error:

E, [2020-03-23 14:07:26#418] ERROR -- : Failed to parse BibTeX on value "--140" (NAME) [#<BibTeX::Bibliography data=[12]>, "@", #<BibTeX::Entry >, {:author=>["Robert E Roth and Andrew W Woodruff and Zachary F Johnson"], :title=>["Value-by-alpha maps: {An} alternative to the cartogram"], :journal=>["The Cartographic Journal"], :year=>["2010"], :volume=>"47", :issue=>"2", :pages=>"130"}]
bibtex.y:138:in on_error': Failed to parse BibTeX on value "--140" (NAME) [#<BibTeX::Bibliography data=[12]>, "@", #<BibTeX::Entry >, {:author=>["Robert E Roth and Andrew W Woodruff and Zachary F Johnson"], :title=>["Value-by-alpha maps: {An} alternative to the cartogram"], :journal=>["The Cartographic Journal"], :year=>["2010"], :volume=>"47", :issue=>"2", :pages=>"130"}] (BibTeX::ParseError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/racc/parser.rb:259:in _racc_do_parse_c'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/racc/parser.rb:259:in do_parse' from bibtex.y:111:in parse'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.2/lib/bibtex/bibliography.rb:67:in parse' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.2/lib/bibtex/bibliography.rb:50:in open'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.2/lib/bibtex/utilities.rb:25:in open' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/bibtex_parser.rb:36:in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/compilers.rb:245:in crossref_from_markdown' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/compilers.rb:21:in generate_crossref'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:95:in compile' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:79:in compile'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

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@arfon arfon commented Mar 23, 2020

@slumnitz - this PR should fix the BibTeX issue here: pysal/splot#104

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@arfon arfon commented Mar 23, 2020

@whedon accept

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@whedon whedon commented Mar 23, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Mar 23, 2020

Reference check summary:

OK DOIs

- 10.1007/978-3-319-50590-9_17 is OK
- 10.1016/j.apgeog.2013.09.012 is OK
- 10.1007/s10109-009-0086-8 is OK
- 10.1007/978-3-319-59511-5_2 is OK
- 10.5281/zenodo.3333010 is OK
- 10.5281/zenodo.3475569 is OK

MISSING DOIs

- https://doi.org/10.1080/01944360802146329 may be missing for title: The Ghost Map: The Story of London’s Most Terrifying Epidemic–and How It Changed Science, Cities, and the Modern World
- https://doi.org/10.1111/j.1435-5597.1988.tb01155.x may be missing for title: Do Spatial Effects Really Matter in Regression Analysis?

INVALID DOIs

- 10.1179/000870409X124887534553372 is INVALID
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@whedon whedon commented Mar 23, 2020

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

Check final proof 👉 openjournals/joss-papers#1388

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1388, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@arfon arfon commented Mar 23, 2020

@slumnitz - could you take a look at the DOI summary above to check to see if the DOIs under MISSING are correct recommendations and also check the INVALID DOI?

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@slumnitz slumnitz commented Mar 23, 2020

@arfon all missing doi's are added and the incorrect one was fixed.

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@arfon arfon commented Mar 23, 2020

@whedon check references

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@whedon whedon commented Mar 23, 2020

Reference check summary:

OK DOIs

- 10.1080/01944360802146329 is OK
- 10.1007/978-3-319-50590-9_17 is OK
- 10.1016/j.apgeog.2013.09.012 is OK
- 10.1111/j.1435-5597.1988.tb01155.x is OK
- 10.1007/s10109-009-0086-8 is OK
- 10.1007/978-3-319-59511-5_2 is OK
- 10.5281/zenodo.3333010 is OK
- 10.5281/zenodo.3475569 is OK
- 10.1179/000870409X12488753453372 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@arfon arfon commented Mar 23, 2020

@whedon accept deposit=true

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@whedon whedon commented Mar 23, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Mar 23, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Mar 23, 2020

🚨🚨🚨 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 👉 openjournals/joss-papers#1389
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01882
  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...

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@arfon arfon commented Mar 23, 2020

@ResidentMario, @martinfleis - many thanks for your reviews here and to @leouieda for editing this submission

@slumnitz - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Mar 23, 2020
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@whedon whedon commented Mar 23, 2020

🎉🎉🎉 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.01882/status.svg)](https://doi.org/10.21105/joss.01882)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01882">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01882/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01882/status.svg
   :target: https://doi.org/10.21105/joss.01882

This is how it will look in your documentation:

DOI

We need your help!

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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@slumnitz slumnitz commented Mar 23, 2020

Thank you for your help and support @leouieda, @martinfleis, @ResidentMario and @arfon.

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@leouieda leouieda commented Mar 26, 2020

@slumnitz congratulations on the publication! Huge thanks to @martinfleis and @ResidentMario for the reviews and @arfon for picking up where I left off (apologies for the disappearance).

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