[REVIEW]: GeoHexViz: A Python package for visualizing hexagonally binned geospatial data

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@mrempel@martinfleis<!--end-editor-- Reviewers: @gassmoeller, @kaustavbhattacharjee Archive: 10.5281/zenodo.7613525

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c051df96dac973486cc312452575e804"><img src="https://joss.theoj.org/papers/c051df96dac973486cc312452575e804/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c051df96dac973486cc312452575e804/status.svg)](https://joss.theoj.org/papers/c051df96dac973486cc312452575e804)

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

@gassmoeller & @kaustavbhattacharjee, 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 @kaustavbhattacharjee

📝 Checklist for @gassmoeller

editorialbot commented 1 year ago

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

For a list of things I can do to help you, just type:

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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 commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.47 s (130.9 files/s, 98355.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              2              1              0          33556
Python                          21           1321           1823           4307
JSON                             5              0              0           1522
Markdown                        12            169              0            892
TeX                              1             45             15            357
reStructuredText                 7            207            195            315
Jupyter Notebook                 6              0           1400            288
YAML                             4              2              4            102
DOS Batch                        1              8              1             26
SVG                              1              0              0             19
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            62           1757           3445          41396
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1807

martinfleis commented 1 year ago

👋🏼 @mrempel, @gassmoeller, @kaustavbhattacharjee 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 https://github.com/openjournals/joss-reviews/issues/5073 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, 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.

Thanks!

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 year ago

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

OK DOIs

- 10.14778/2733004.2733035 is OK
- 10.1109/TVCG.2011.185 is OK
- 10.1186/1475-2875-2-36 is OK
- 10.1016/j.ijar.2009.05.011 is OK
- 10.1559/152304092783721231 is OK
- 10.1109/38.865878 is OK
- 10.1016/j.ecolmodel.2007.03.041 is OK
- 10.1016/j.ecolmodel.2007.03.041 is OK
- 10.1080/15230406.2016.1180263 is OK
- 10.1002/geo2.46 is OK
- 10.1145/3453892.3461336 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kaustavbhattacharjee commented 1 year ago

Okay. Thanks for the update.

kaustavbhattacharjee commented 1 year ago

Review checklist for @kaustavbhattacharjee

Conflict of interest

[x] 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

[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 https://github.com/mrempel/geohexviz?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mrempel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

gassmoeller commented 1 year ago

Review checklist for @gassmoeller

Conflict of interest

[x] 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

[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 https://github.com/mrempel/geohexviz?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mrempel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

gassmoeller commented 1 year ago

@mrempel: I am going through the review checklist right now and have a question concerning the following criteria:

 Contribution and authorship: Has the submitting author (@mrempel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Based on the repository insights it looks like @tony-zeidan contributed most of the software and the first draft of the paper, and you finalized the paper and prepared the repository for submission to JOSS. Could I get confirmation from @tony-zeidan that this is the case and that you both collaborated on the software and agreed on the submission?

gassmoeller commented 1 year ago

@mrempel and @tony-zeidan: I went through the review checklist and wanted to congratulate you for this nicely written and documented piece of software. I think it already fulfills almost all the criteria for publication by JOSS and if you address the minor issues I raised in the repository the publication should be good to go. On a side note I think the main challenge for you going forward will be to keep it compatible to the numerous packages you depend on, I already see a number of deprecation warnings when executing the examples (let me know if you want me to post them as an issue). Anyway I hope you can keep the project alive and I may actually make use of it for some of my own work, although my community usually relies more on continuous interpolated maps.

mrempel commented 1 year ago

@gassmoeller - In regards to your question about contribution and authorship, @tony-zeidan was my co-op student between Feb 2021 and Dec 2021. It is correct that Tony implemented the majority of the code within GeoHexViz; I conceived the software and its design requirements (based on previous research I published with colleagues, see Figure 8 in https://cradpdf.drdc-rddc.gc.ca/PDFS/unc356/p812844_A1b.pdf), defined the functional specification, selected and crafted the examples in the repository, helped Tony resolve issues during implementation, and drafted the article for this submission. As my student, it was Tony's responsibility to implement the code and manage the git repository (I provided Tony the manuscript to include in the repository) to provide him with experience in doing so. Upon completion of his co-op term, Tony transferred the repository to me to complete the submission to this journal.

I hope this helps - if you need further information, please do not hesitate to let me know.

tony-zeidan commented 1 year ago

@gassmoeller Hi there! I can confirm what @mrempel stated in his reply to your question is indeed correct.

As to the deprecation warnings I'm sad to hear that but I'm pretty sure most of them are due to iterating over objects in a way that won't be supported going forward. These should be easy to fix. I could use a log of depreciation warnings to get an idea...

I look forward to seeing your GeoHexViz visualizations!

gassmoeller commented 1 year ago

@tony-zeidan & @mrempel thanks for the confirmation that is what I was thinking, I just wanted to make sure I had checked it properly. Also thanks for addressing all my comments on the code. @martinfleis: In my opinion this is now ready for publication within JOSS.

tony-zeidan commented 1 year ago

@gassmoeller We are very excited! Thank you for raising the issues with our software and bringing them to our attention.

martinfleis commented 1 year ago

Thank you @gassmoeller!

Will wait for the second reviewer @kaustavbhattacharjee now to deliver their comments.

kaustavbhattacharjee commented 1 year ago

@martinfleis I have completed my review, and I think this is ready for publication within JOSS. I was able to run the program quite easily. Here are a few minor comments for the authors @mrempel @tony-zeidan :

I had some doubts about the contributions of @mrempel. But it was clarified through the previous conversation on this thread.
The image bombings.pdf is not rendered properly in paper.md. I would recommend either converting it to an image or embedding PDF using HTML code.
I was also wondering if this package can be published to PyPI so that users can install it directly through pip

tony-zeidan commented 1 year ago

@kaustavbhattacharjee We are glad to hear from you!

We are going to address your comments as soon as possible. The bombings.pdf issue can be fixed quickly, however there are some issues for us that come along with publishing the package to PyPI. We will go this route as soon as possible.

martinfleis commented 1 year ago

there are some issues for us that come along with publishing the package to PyPI

Can you elaborate? We may be able to help here. I would very much like to see the package published there before the acceptance, even though it is not a formal requirement of the JOSS.

mrempel commented 1 year ago

@martinfleis @kaustavbhattacharjee - Regarding the two latter comments from @kaustavbhattacharjee:

Figure in paper.md: The figure has been changed from a PDF to PNG, and thus now renders properly (both in the a browser and in the compiled PDF). This has been pushed to the master branch.
Publish to PyPI: The difficulty that Tony was referring to was that geopandas is more difficult to install from pip, and our install process uses the conda-forge channel. That said, we have now pushed GeoHexViz to PyPI (see https://pypi.org/project/geohexviz/) and the install instructions have been modified to provide two options - install from PyPI (option 1), and install from GitHub (option 2). Option 1 requires the user to install geopandas separately, and instructions are provided in README.rst to acomplish this task.

Please let us know if there are any further questions or comments regarding our submission.

martinfleis commented 1 year ago

As a geopandas maintainer I think I know what you're talking about :). Thanks for pushing it to PyPI! Do you also want to make it available on conda-forge? Happy to help setting up the recipe.

mrempel commented 1 year ago

@tony-zeidan and I were talking about that - it is an enhancement listed in our issues - but didn't want to delay the final decision regarding publication. If it possible to make it available on conda-forge without too much work, then we would be happy to do it and any help setting up a recipe would be appreciated.

martinfleis commented 1 year ago

@mrempel I'll have a look and let you know, it is not that much work. We don't have to wait with the acceptance for it though :).

Thank you @gassmoeller and @kaustavbhattacharjee for your reviews!

The submission is now almost ready to be published.

@mrempel the next steps you need to do now:

[x] 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.
[x] Archive the reviewed software in Zenodo or a similar service
[x] 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.
[x] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

mrempel commented 1 year ago

DOI of the archived version is 10.5281/zenodo.7613525.

mrempel commented 1 year ago

@martinfleis - I am having trouble checking the boxes for "Archive the reviewed software" and "Please list the DOI" in the above comment - these are both done. You can find the archive at https://zenodo.org/record/7613525, and the DOI is listed in the above comment.

martinfleis commented 1 year ago

@editorialbot set v1.0.2 as version

editorialbot commented 1 year ago

Done! version is now v1.0.2

martinfleis commented 1 year ago

@editorialbot set 10.5281/zenodo.7613525 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7613525

martinfleis commented 1 year ago

@mrempel thank you! Can you please manually edit the title of the Zenodo archive to match the title of the paper? (GeoHexViz: A Python package for visualizing hexagonally binned geospatial data)

martinfleis commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

martinfleis commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.14778/2733004.2733035 is OK
- 10.1109/TVCG.2011.185 is OK
- 10.1186/1475-2875-2-36 is OK
- 10.1016/j.ijar.2009.05.011 is OK
- 10.1559/152304092783721231 is OK
- 10.1109/38.865878 is OK
- 10.1016/j.ecolmodel.2007.03.041 is OK
- 10.1016/j.ecolmodel.2007.03.041 is OK
- 10.1080/15230406.2016.1180263 is OK
- 10.1002/geo2.46 is OK
- 10.1145/3453892.3461336 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mrempel commented 1 year ago

@martinfleis - I have updated the title in Zenodo as required.

martinfleis commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

martinfleis commented 1 year ago

@mrempel thank you! It is all done from my side and I have passed the paper onto the editor in chief for the final check and acceptance. Congrats!

editorialbot commented 1 year ago

:wave: @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3945, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 year ago

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

OK DOIs

- 10.14778/2733004.2733035 is OK
- 10.1109/TVCG.2011.185 is OK
- 10.1186/1475-2875-2-36 is OK
- 10.1016/j.ijar.2009.05.011 is OK
- 10.1559/152304092783721231 is OK
- 10.1109/38.865878 is OK
- 10.1016/j.ecolmodel.2007.03.041 is OK
- 10.1016/j.ecolmodel.2007.03.041 is OK
- 10.1080/15230406.2016.1180263 is OK
- 10.1002/geo2.46 is OK
- 10.1145/3453892.3461336 is OK

MISSING DOIs

- None

INVALID DOIs

- None

arfon commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3969
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05073
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 1 year ago

@gassmoeller, @kaustavbhattacharjee – many thanks for your reviews here and to @jmschrei 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 ✨

@mrempel – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 1 year ago

: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.05073/status.svg)](https://doi.org/10.21105/joss.05073)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05073">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05073/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05073/status.svg
   :target: https://doi.org/10.21105/joss.05073

This is how it will look in your documentation:

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