[REVIEW]: TessPy: a python package for geographical tessellation

[editorialbot]

Submitting author: @siavash-saki (Siavash Saki)
Repository: https://github.com/siavash-saki/tesspy
Branch with paper.md (empty if default branch):
Version: v0.1.2
Editor: @martinfleis
Reviewers: @jGaboardi, @BenjMy
Archive: 10.5281/zenodo.7016503

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c90e8d78b221d037f366e5fd1f61a7de/status.svg)](https://joss.theoj.org/papers/c90e8d78b221d037f366e5fd1f61a7de)

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

@jGaboardi, 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 @martinfleis 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 @jGaboardi

📝 Checklist for @BenjMy

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.35 s (52.4 files/s, 130725.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             3              0              0         141583
JavaScript                      13           2405           2470           9222
HTML                            19            885             57           8162
SVG                              1              0              0           2671
Python                           9            379            517           1232
CSS                              4            191             35            759
Jupyter Notebook                 9              0           5203            620
Markdown                         3             63              0            153
TeX                              1             18              0            150
reStructuredText                 6             72             44             79
DOS Batch                        1              8              1             26
YAML                             1              1              4             18
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            71           4026           8338         164684
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1110

[editorialbot]

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

OK DOIs

- 10.1016/j.tra.2016.01.014 is OK
- 10.3390/rs12020229 is OK
- 10.21105/joss.00215 is OK
- 10.21105/joss.01807 is OK
- 10.48718/7jjr-1c66 is OK
- 10.5281/zenodo.3483425 is OK
- 10.1080/10095020.2016.1146440 is OK
- 10.1016/s0022-1694(00)00144-x is OK
- 10.1016/j.compenvurbsys.2007.11.002 is OK
- 10.1145/2030112.2030126 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[martinfleis]

@editorialbot add @BenjMy as reviewer

[editorialbot]

@BenjMy added to the reviewers list!

[martinfleis]

👋🏼 @siavash-saki, @jGaboardi, @BenjMy, this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers should create checklists with the JOSS requirements using the command @editorialbot generate my checklist. 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 small pull requests if needed) on the software repository. When doing so, please mention #4620 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 2-4 weeks (but considering the summer we can wait a bit longer), feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

[jGaboardi]

Review checklist for @jGaboardi

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/siavash-saki/tesspy?
• 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 (@siavash-saki) 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, 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?

[BenjMy]

Review checklist for @BenjMy

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/siavash-saki/tesspy?
• 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 (@siavash-saki) 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, 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?

[jGaboardi]

@siavash-saki @martinfleis

I have completed an initial pass for tesspy.

This package has the potential to make an immediate impact in the scientific & spatial/geographic communities. There are thoughtful and well-paced tutorial notebooks that provide high-level introductions and more detailed examples for the various tessellation methods offered in tesspy. I am excited both for the potential of the package in the long run and possibly to use it in the immediate future. (Also, very cool logo).

Below are some of my initials thoughts from the checklist, etc. that I will begin creating issues for and linking back to this comment.

Checklist topics

• General Checks
  • Contribution and authorship
    • Unclear what role Tobias Hagen has played in the code development (no commits).
    • The repo only 2 PRs; Is there a previous version that is private?
• Functionality
  • Installation
    • Install proceeds as planned (on conda-forge). However, tests can't be run out of the box. There needs to testing requirements. What do the authors use to run testing? Maybe pytest?
  • Functionality
    • Tests do not pass locally for me (see below). I need to see all tests passing before digging deeper into functionality.
• Documentation
  • A statement of need
    • The authors define the problem being solved in the docs/README but don't identify the target audience.
  • Functionality documentation
    • [JOSS] Documentation consistency siavash-saki/tesspy#8
  • Automated tests
    • There are tests but they are failing for me locally. I installed following the conda instructions.
    • See [JOSS] Test suite failing siavash-saki/tesspy#6 for more information.
  • Community guidelines?
    • [JOSS] Expand on Community guidelines siavash-saki/tesspy#7
• Software paper
  • Overall it is good start, but reads a bit choppy. There are frequent examples of short sentences that can be combined for readability and clarity. To reiterate, the paper is a good place as a starting point, but should be fleshed out and smoothed.
  • [JOSS] Paper edits, etc. siavash-saki/tesspy#12
  • [JOSS] State of the field / References siavash-saki/tesspy#13
• Misc. consider implementing these before making more substantive changes
  • [JOSS] Rename default branch siavash-saki/tesspy#4
  • [JOSS] Code formatting in repo? siavash-saki/tesspy#5

[siavash-saki]

@jGaboardi

Thank you for carefully reviewing our code and manuscript. We are pleased by your enthusiasm for tesspy and thank you for the insightful comments. We could definitely improve tesspy according to the issues that you opened.

I can answer some of your general questions here:

• Unclear what role Tobias Hagen has played in the code development (no commits).

Tobias Hagen is the project manager of the research project. He has advised and supervised the other two authors along the entire process of code development. His contribution to the TessPy package is raising the research question, pointing out the need for code development, supporting in finding conceptual solutions, reviewing and commenting on ideas and tasks, testing the code on real-world data and checking the usefulness of the code in concrete applications.

• The repo only 2 PRs; Is there a previous version that is private?

The initial version was developed for some parts locally. After that, there were a lot of commits directly to the master branch. But we recently followed the best practice to create, review, and merge Prs.

• Install proceeds as planned (on conda-forge). However, tests can't be run out of the box. There needs to testing requirements. What do the authors use to run testing? Maybe pytest?

We have used pytest.

• Tests do not pass locally for me (see below). I need to see all tests passing before digging deeper into functionality.

We will review the tests and make the necessary changes to ensure they all pass.

Regarding Documentation, Software paper, and Misc:
We will work on the issues in the next days and incorporate the points you mentioned.

[martinfleis]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.tra.2016.01.014 is OK
- 10.3390/rs12020229 is OK
- 10.1016/j.softx.2018.12.005 is OK
- 10.21105/joss.00215 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.5281/zenodo.5139815 is OK
- 10.21105/joss.01807 is OK
- 10.48718/7jjr-1c66 is OK
- 10.21105/joss.00205 is OK
- 10.5281/zenodo.3483425 is OK
- 10.5281/zenodo.6326050 is OK
- 10.1080/10095020.2016.1146440 is OK
- 10.1016/s0022-1694(00)00144-x is OK
- 10.5281/zenodo.6946292 is OK
- 10.52324/001c.8285 is OK
- 10.1111/gean.12276 is OK
- 10.21105/joss.03092 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v012.i06 is OK
- 10.25436/E2Z59N is OK
- 10.1016/j.compenvurbsys.2007.11.002 is OK
- 10.1145/2030112.2030126 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[martinfleis]

Thank you all!

@siavash-saki The submission is now almost ready to be published.

The next steps you need to do now:

• Make a new tagged release (or let me know if the latest one contains all the changes) of the software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service
• Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[siavash-saki]

@martinfleis

• A new tagged release v0.1.2 with the latest changes is created.
• The reviewed software (latest release) is archived in Zenodo.
• Metadata is modified and checked. The title and author list match the metadata of the paper.
• DOI of the archived version in Zenodo: 10.5281/zenodo.7016503

[martinfleis]

@editorialbot set 10.5281/zenodo.7016503 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7016503

[martinfleis]

@editorialbot set v0.1.2 as version

[editorialbot]

Done! version is now v0.1.2

[martinfleis]

@editorialbot generate pdf

[editorialbot]

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

[martinfleis]

Thank you @siavash-saki! I'm going to hand this over now to the associate EiC on rotation for the final steps.

[martinfleis]

@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.tra.2016.01.014 is OK
- 10.3390/rs12020229 is OK
- 10.1016/j.softx.2018.12.005 is OK
- 10.21105/joss.00215 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.5281/zenodo.5139815 is OK
- 10.21105/joss.01807 is OK
- 10.48718/7jjr-1c66 is OK
- 10.21105/joss.00205 is OK
- 10.5281/zenodo.3483425 is OK
- 10.5281/zenodo.6326050 is OK
- 10.1080/10095020.2016.1146440 is OK
- 10.1016/s0022-1694(00)00144-x is OK
- 10.5281/zenodo.6946292 is OK
- 10.52324/001c.8285 is OK
- 10.1111/gean.12276 is OK
- 10.21105/joss.03092 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v012.i06 is OK
- 10.25436/E2Z59N is OK
- 10.1016/j.compenvurbsys.2007.11.002 is OK
- 10.1145/2030112.2030126 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3460, 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.04620 joss-papers#3477
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04620
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]

@jGaboardi, @BenjMy – many thanks for your reviews here and to @martinfleis 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 ✨

@siavash-saki – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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HTML:
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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04620/status.svg
   :target: https://doi.org/10.21105/joss.04620

This is how it will look in your documentation:

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[siavash-saki]

@jGaboardi @BenjMy @martinfleis
I sincerely appreciate the time and effort you put into reviewing the submissions (especially our submission). Publishing in JOSS was a unique experience, and the review process was extremely smooth and helpful.
We would be more than happy if we could ever contribute to JOSS. (Donation is already made) :D
I wish you all the best.