Joss-reviews: [REVIEW]: swisslandstats-geopy: Python tools for the land statistics datasets from the Swiss Federal Statistical Office

[whedon]

Submitting author: @martibosch (Martí Bosch)
Repository: https://github.com/martibosch/swisslandstats-geopy
Version: 0.7.2
Editor: @leouieda
Reviewer: @weikang9009, @darribas
Archive: 10.5281/zenodo.3387312

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/b6de0f096382d4dcd5d137a3f1edcb30/status.svg)](http://joss.theoj.org/papers/b6de0f096382d4dcd5d137a3f1edcb30)

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

@weikang9009 & @darribas, 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 @weikang9009

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: 0.7.2
• [x] Authorship: Has the submitting author (@martibosch) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @darribas

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: 0.7.2
• [x] Authorship: Has the submitting author (@martibosch) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @weikang9009, @darribas it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

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:

1. 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[leouieda]

:wave: @weikang9009 @darribas @martibosch this is the review thread for the swisslandstats-geopy paper. All of our communications will happen here from now on.

Both @weikang9009 and @darribas 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#1511 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 2-4 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.

[leouieda]

:wave: Hi @weikang9009 and @darribas just checking in on the progress of the reviews. I see some issues have been opened (and resolved) in the project repository. Please let me know what your current status is and any hangups in the review that might need to be resolved.

[weikang9009]

Hi @leouieda, I am almost done with the review. @martibosch has been very responsive in resolving the issues I opened. I just opened two issues related to adding a statement of the target audience and missing DOIs in the paper.

[leouieda]

@weikang9009 thanks for the update and opening all those issues :+1: Let me know when you have a final verdict (meaning that the software passes all requirements)

[darribas]

HEllo! Sorry for the delay, getting on the review now, should be able to turn it around rather quickly!

@leouieda somehow I can't cross-out items on the checklist 🤔 Could it be because I'm not assigned to this issues? Nevermind, just figured it out :-)

[weikang9009]

Hi @leouieda, the package was updated and a new version (V0.7.1) was released on github and pypi 7 days ago by @martibosch. Since this most recent version does not match the one given in the review points (shown below), I am not sure how to deal with this?

• [ ] Version: Does the release version given match the GitHub release (v0.6.1)?

[leouieda]

@darribas thanks for the update :+1:

@weikang9009 that happens when there is a release while the review is ongoing. As long as the version is close and matches the Github release/tag, then it should be OK. We'll update the version information prior to publication.

[darribas]

On the authorship, @martibosch has clearly contributed to the package. In fact, he's the only contributor). The second author has not. Usually, this would point to lack of substantive contribution but I could see how this is also reasonable if the second author has provided guidance, technical support, etc. Happy to check that one off if @martibosch agrees.

[darribas]

OK that's my review for now @martibosch. Such a cool little package!!!

[martibosch]

Regarding the comment on authorship: this library has been created in the context of my PhD thesis, which is why I included my thesis supervisor as second author. Nevertheless, since this paper is not central to my thesis it is not necessary that he appears here as I am indeed the sole contributor to the library. I have therefore changed the paper accordingly in 1c8f888

[leouieda]

@martibosch we don't require all authors to be package contributors since there are non-code contributions that merit authorship but aren't registered in the git log. I'll leave the final decision up to you.

[darribas]

Yes, my question wasn't a demand but much more in line with @leouieda's view. It was just raising bringing it up...

[martibosch]

well I believe that in this case, leaving it to one author is more coherent with the JOSS autorship guidelines.

[leouieda]

:wave: @weikang9009 and @darribas please have a final look to see if all your comments have been addressed.

@darribas I see that there are some unchecked items in your reviewer checklist. Are these still in progress or have they been satisfied with the recent changes?

[darribas]

Completed now, good good to go!

[weikang9009]

Also good to go from my side!

[leouieda]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[leouieda]

@martibosch I submitted a PR with a few minor fixes to the JOSS paper. Please let me know when you merge it and we can move on with the publication.

[martibosch]

@leouieda thank you for your corrections. I have already reviewed and merged the PR with your fixes.
Martí

[labarba]

Is this submission ready for the final checks before acceptance?

[leouieda]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[leouieda]

@labarba thank you for the nudge, it's completely my fault that this hasn't moved along. I made one final editorial PR to the paper. After that, this should be good to go.

[leouieda]

@martibosch I'm happy say that your paper is ready for publication in JOSS! :tada: Here are the final steps you need to take:

• Double check authors and affiliations (including ORCIDs)
• Make a release with the latest changes from the review and post the version number here.
• Archive the release on Zenodo/figshare and post the DOI here (make sure the title and author list matches the JOSS paper, if possible).

[martibosch]

• [x] Double check authors and affiliations (including ORCIDs)

Done

• [ ] Make a release with the latest changes from the review and post the version number here.

The latest release is 0.7.1, and all the subsequent commits have been amendments to the paper/README and including the "examples" folder in the GitHub repository (however, such folder is not included in the MANIFEST), therefore nothing would change in an hypothetical new release (well, the README would be different - but that does not seem to justify a release in semantic versioning). Shall we leave it like that, or release a patch (i.e., 0.7.2) with the above changes?

• [ ] Archive the release on Zenodo/figshare and post the DOI here (make sure the title and author list matches the JOSS paper, if possible).

Once the second task is done, I will proceed with the third and last one.

[leouieda]

@martibosch it would be best to have a patch release if possible. You might want to take this opportunity to set the citation information for the package to the JOSS paper (the doi will be 10.21105.joss.01511) and have it registered in the release.

[martibosch]

I have released 0.7.2 and archived it to Zenodo https://doi.org/10.5281/zenodo.3387312 (with the matching title and author list).

[leouieda]

@whedon set 0.7.2 as version

[whedon]

OK. 0.7.2 is the version.

[leouieda]

@whedon set 10.5281/zenodo.3387312 as archive

[whedon]

OK. 10.5281/zenodo.3387312 is the archive.

[leouieda]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1109/MCSE.2011.37 is OK
• 10.1016/j.compenvurbsys.2017.05.004 is OK
• 10.2785/132365 is OK
• 10.25080/Majora-4af1f417-011 is OK
• 10.3334/ORNLDAAC/1570 is OK
• 10.1007/s10980-019-00850-7 is OK
• 10.1101/645549 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[leouieda]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[leouieda]

@martibosch thank you for the updates. Everything looks good to go now :confetti_ball:

[leouieda]

@openjournals/joss-eics this submission is ready for publication

[arfon]

:wave: @Kevin-Mattheus-Moerman - do you want to do the final checks on this submission?

[Kevin-Mattheus-Moerman]

@martibosch can you check/work on the following points in relation to your paper:

• [x] We are about to process this submission for acceptance. Can you please thoroughly read and double check the paper? Also ensure all author names and affiliations are accurate and that acknowledgements to contributors and funding sources have been added.
• [x] Can you remove the acronyms from your affiliations (I would keep them if they are used in the text but since they are not you can remove them).
• [x] In "..are rarely capable of processing such format.". Please consider using "formats" or "a format".
• [x] Does NumPy need its own independent reference?
• [x] Although usable are you able to improve the resolution of figure 1 (its a bit fuzzy)?
• [x] Fix the word nevertheless in"Neverhteless, although other...."
• [x] Once you have complete the above, please run @whedon generate pdf here to update your proofs

[Kevin-Mattheus-Moerman]

@leouieda can you verify the above points and ping me once we are ready to proceed? Thanks

[martibosch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[martibosch]

• [x] We are about to process this submission for acceptance. Can you please thoroughly read and double check the paper? Also ensure all author names and affiliations are accurate and that acknowledgements to contributors and funding sources have been added.

• [x] Can you remove the acronyms from your affiliations (I would keep them if they are used in the text but since they are not you can remove them).

• [x] In "..are rarely capable of processing such format.". Please consider using "formats" or "a format".

• [x] Does NumPy need its own independent reference?

Well, I believe that since pandas, shapely and OSMnx have their own independent reference, NumPy should be treated equally. But this can be changed if you consider it more appropriate.

• [x] Although usable are you able to improve the resolution of figure 1 (its a bit fuzzy)?

I have changed the respective code snippets in the paper so that the full extent of the canton of Vaud is plotted. I believe it might be a bit too big now. I can amend the commit with a smaller figure if you consider it more appropriate.

• [x] Fix the word nevertheless in"Neverhteless, although other...."
• [x] Once you have complete the above, please run @whedon generate pdf here to update your proofs

[leouieda]

Well, I believe that since pandas, shapely and OSMnx have their own independent reference, NumPy should be treated equally. But this can be changed if you consider it more appropriate.

I agree that numpy deserves a citation.

I have changed the respective code snippets in the paper so that the full extent of the canton of Vaud is plotted. I believe it might be a bit too big now. I can amend the commit with a smaller figure if you consider it more appropriate.

The figure size is fine but the resolution is a bit low (which I think was the original criticism). If you could please save it with a higher DPI, that would solve the problem.

[martibosch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[martibosch]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[martibosch]

I have upgraded the DPI of the figure and amended the commit. I believe that the plot for the full canton of Vaud is more aesthetically pleasing, so I have kept such change (regardless of the DPI).

[leouieda]

Thank you @martibosch, the figure looks much better now :+1:

@Kevin-Mattheus-Moerman I believe all points have been addressed and we should be ready to move forward.

[Kevin-Mattheus-Moerman]

@martibosch thanks for making those changes. It looks good now.

[Kevin-Mattheus-Moerman]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1109/MCSE.2011.37 is OK
• 10.1016/j.compenvurbsys.2017.05.004 is OK
• 10.2785/132365 is OK
• 10.25080/Majora-4af1f417-011 is OK
• 10.3334/ORNLDAAC/1570 is OK
• 10.1007/s10980-019-00850-7 is OK
• 10.1101/645549 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[Kevin-Mattheus-Moerman]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/962

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/962, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/963
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01511
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...

[Kevin-Mattheus-Moerman]

@arfon, still a 404 it seems, on the DOI. I'll check again later.

[arfon]

@arfon, still a 404 it seems, on the DOI. I'll check again later.

Looks like there was a minor issue with the paper (no affiliation index) which for some reason Whedon failed silently on. I've fixed this now.

[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.01511/status.svg)](https://doi.org/10.21105/joss.01511)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01511">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01511/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01511/status.svg
   :target: https://doi.org/10.21105/joss.01511

This is how it will look in your documentation:

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