[REVIEW]: GemGIS - Spatial Data Processing for Geomodeling

[whedon]

Submitting author: @AlexanderJuestel (Alexander Jüstel)
Repository: https://github.com/cgre-aachen/gemgis
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @crvernon
Reviewers: @omshinde, @kanishkan91
Archive: 10.5281/zenodo.6511767

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/5855a6fc36e3a33c4014b3afa535b348/status.svg)](https://joss.theoj.org/papers/5855a6fc36e3a33c4014b3afa535b348)

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

@omshinde & @kanishkan91, 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 @crvernon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @omshinde

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@AlexanderJuestel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @kanishkan91

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@AlexanderJuestel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @omshinde, @kanishkan91 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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[crvernon]

👋 @omshinde @kanishkan91 @AlexanderJuestel - the review takes place in this issue.

[crvernon]

Also, please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://github.com/cgre-aachen/gemgis repository. This will help everyone have a single point of reference.

[AlexanderJuestel]

@crvernon, thanks for assisting with this!
@omshinde, @kanishkan91, I am looking forward to go through this review with you guys!

[AlexanderJuestel]

@crvernon is there anything that I can do in the meantime or do we have to wait for @omshinde and @kanishkan91 to start the review?

[crvernon]

Thanks for checking in @AlexanderJuestel - at this point we will wait on the first round of feedback to come in as issues/comments. You can address these as they come up to expedite the process. I'll periodically send out check-in comments that open up lines for us to communicate any blockers to progress.

[kanishkan91]

@whedon generate pdf

[whedon]

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

[kanishkan91]

@AlexanderJuestel I've started the review. I had some very minor questions for you related to the repository to start with (mostly related to the initial checks),

1. Firstly, there are two pull requests that are open here. Do these need to be merged in? Just wanted to confirm.
2. I looked at the recent commit history. It looked like the recent commits were mostly from yourself and @RichardScottOZ. Could you describe the roles that the other co-authors played in the development of the software repository?
3. Also, in the pydocs, the main developers from the pydocs file - https://gemgis.readthedocs.io/en/latest/getting_started/authors.html don't all appear as co-authors in the paper. Is this intentional? This being a software paper, ideally all major contributors to software development that are mentioned in the docs should be co-authors.
4. The license you use is GNU LESSER GENERAL PUBLIC LICENSE. My understanding is limited here, but a GPL license would impose some copy left restrictions on the users (they would have to ensure that they release anything that uses GemGIS as a freely available open source software package). Is this intentional? I have seen packages use BSD2 in its place which offers more flexibility to the end user. @crvernon Do you have any thoughts on this?

Once again, I just wanted to post these here since they are related to the initial checks.

[AlexanderJuestel]

@kanishkan91, thanks for getting started on the review. Regarding your comments:

1. I merged one of the PRs but would like to keep the second one open as we may change some of the tutorial notebooks during the review process here in combination with updating the documentation.

2. @RichardScottOZ is a very active user providing always great feedback on typos and grammatical errors in the docstrings or notebooks. However, he has not played an active role in the development of the software yet.

3. Good point. As for @RichardScottOZ, @Japhiolite provided great feedback on the code and the documentation, mostly offline, but did not provide any functionality for the software. I would add 'Marius Pischke' and 'Miguel de la Varga' as authors to the documentation and change the status of @RichardScottOZ and @Japhiolite.

[AlexanderJuestel]

@kanishkan91 I just fixed the authors in the docs. The current build of the documentation is failing though, so changes are only visible locally right now but let's tackle one thing at a time :)

[kanishkan91]

@AlexanderJuestel Thanks. For my point no 2 from above, could you describe the roles the different co-authors played in the development of the software? This does not need to be a part of the paper or repo but having those descriptions here in the review thread would suffice.

[AlexanderJuestel]

@kanishkan91, I am the main developer of the software and added most of the functionality of the package. @endarthur contributed with helpful tips with respect to the implementation of certain functionality. He basically helped me to make things run. Marius Pischke developed with me functionality within the framework of his master thesis at RWTH Aachen University, which I then implemented in GemGIS as he does not have a Github account. @Leguark is the main developer for the GemPy package (https://github.com/cgre-aachen/gempy). Without his developments, GemGIS would not have a purpose. He also contributed minor things to GemGIS as well. @flohorovicic is/was my supervisor who highly encouraged me to develop GemGIS. @Japhiolite and @RichardScottOZ mainly provided feedback on the documentation and notebooks and also provided feedback on other communication channels.

Would this description be sufficient or do you need any more information or statements of the respective persons?

[kanishkan91]

@AlexanderJuestel This is sufficient. Thanks.

[crvernon]

📣 Mid-week rally! Just checking in to see how things are going.

👐 @kanishkan91 thanks for kicking off this review!

@omshinde how are things going? The author @AlexanderJuestel has been very responsive if you have any questions.

Have a great and productive rest of the week!

[whedon]

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

[whedon]

👋 @kanishkan91, please update us on how your review is going (this is an automated reminder).

[omshinde]

@crvernon Thanks for the reminder. I just finished my other JOSS review and would be able to progress fast with GemGIS submission now. I am very excited and looking forward.

[crvernon]

📣 Hope all is progressing smoothly.

👋 @kanishkan91 and @omshinde could you update me on your progress? Thanks!

[omshinde]

@whedon generate pdf

[whedon]

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

[AlexanderJuestel]

@crvernon I have finally gotten the go-ahead from my institute. I just had to edit the affiliations a little and one citation.

Please proceed with the publication!
Cheers Alex

[AlexanderJuestel]

@crvernon any news from your side on the progress of the publication? :)

[crvernon]

Yes @AlexanderJuestel I'll set things in order the first of next week.

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.4569086 is OK
- 10.5281/zenodo.4459137 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.4572994 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5194/gmd-14-5063-2021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@AlexanderJuestel we are almost there! Next is just setting up the archive for your new release.

• We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

• Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list. You may also add the authors' ORCID.
• Please list the DOI of the archived version here

I can then move forward with accepting the submission.

[AlexanderJuestel]

Hi @crvernon,

please find the archived version of GemGIS here under this DOI Number: https://doi.org/10.5281/zenodo.6511767

[crvernon]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[crvernon]

@editorialbot set 10.5281/zenodo.6511767 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6511767

[crvernon]

@AlexanderJuestel - thanks for putting together a really nice software product! Thanks to @omshinde and @kanishkan91 for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@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

- 10.5281/zenodo.4569086 is OK
- 10.5281/zenodo.4459137 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.4572994 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5194/gmd-14-5063-2021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3185

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3185, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

@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.03709 joss-papers#3192
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03709
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...

[AlexanderJuestel]

@crvernon, thank you for serving as editor for this paper!

@omshinde, @kanishkan91, thank you very much for your reviews and the time you put in it!

We finally did it!
Alex

[kyleniemeyer]

Congratulations @AlexanderJuestel on your article's publication in JOSS!

Many thanks to @omshinde and @kanishkan91 for reviewing this, and @crvernon for editing.

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03709/status.svg)](https://doi.org/10.21105/joss.03709)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03709/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03709/status.svg
   :target: https://doi.org/10.21105/joss.03709

This is how it will look in your documentation:

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