[REVIEW]: GemGIS - Spatial Data Processing for Geomodeling

whedon commented 3 years ago

Submitting author: !--author-handle-->@AlexanderJuestel@crvernon<!--end-editor-- Reviewers: @omshinde, @kanishkan91 Archive: 10.5281/zenodo.6511767

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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:

Make sure you're logged in to your GitHub account
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

[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 repository url?
[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 (@AlexanderJuestel) 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

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 and who the target audience is?
[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?

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

[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 repository url?
[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 (@AlexanderJuestel) 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

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 and who the target audience is?
[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?

crvernon commented 2 years ago

:mega: Mid-week rally!

It would be good to get this one wrapped up soon @AlexanderJuestel so we can free up our reviewers. How are things looking on your side of things for finishing up the remaining issues? It looks like both @kanishkan91 and @omshinde are waiting on responses to proceed.

Thanks!

AlexanderJuestel commented 2 years ago

Hey everyone, I totally agree. I am back from vacation next week and will tackle the open issues right away then and hope to solve everything by the end of next weekend

AlexanderJuestel commented 2 years ago

@crvernon I still have an issue with the documentation, The fixed will be delayed a little, sorry

crvernon commented 2 years ago

@AlexanderJuestel - please provide me with an update of your status and a timeline of when you will be able to complete your revisions. Thanks!

AlexanderJuestel commented 2 years ago

@crvernon Right now, I am not sure when I can complete them. I have issues with the documentation that I am currently not able to fix.

AlexanderJuestel commented 2 years ago

@crvernon I will try to port the documentation to another service and hope to make it run that way!

crvernon commented 2 years ago

Ok @AlexanderJuestel please let me know if you need assistance with this.

crvernon commented 2 years ago

@AlexanderJuestel please let me know the status of your changes. We should try to wrap this up ASAP. Thanks!

AlexanderJuestel commented 2 years ago

I will give the docs another try @crvernon, so hopefully, they will build now!

AlexanderJuestel commented 2 years ago

@crvernon I managed to get my documentation running again, finally. I am trying now to finish the remaining open remarks of @omshinde and @kanishkan91

AlexanderJuestel commented 2 years ago

@omshinde, I would like to ask you to check the following points off your checklist:

Functionality documentation: I was just able to build the documentation again. See for example https://readthedocs.org/projects/gemgis/builds/16267667/
Automated tests: Automated tests are implemented using Github Actions. See https://github.com/cgre-aachen/gemgis/blob/main/.github/workflows/testing.yml
Community Guidelines: Please see the contributing document for that: https://github.com/cgre-aachen/gemgis/blob/main/CONTRIBUTING.md
Statement of Need: The statement of need was added to the paper. See https://github.com/cgre-aachen/gemgis/actions/runs/1934016389 to download the latest version Also see here
Quality of Writing: Please check that if there is nothing to improve

AlexanderJuestel commented 2 years ago

@kanishkan91 I would like to ask you to check the following points off your checklist:

Example usage: Here you can find many examples of using GemGIS: https://gemgis.readthedocs.io/en/latest/getting_started/tutorial/index.html
Functionality documentation: I was just able to build the documentation again. See for example https://readthedocs.org/projects/gemgis/builds/16267667/
Community Guidelines: Please see the contributing document for that: https://github.com/cgre-aachen/gemgis/blob/main/CONTRIBUTING.md

crvernon commented 2 years ago

:wave: @kanishkan91 and @omshinde please see @AlexanderJuestel comments above and feel free to post any questions.

kanishkan91 commented 2 years ago

@AlexanderJuestel , @crvernon Thanks. I'l complete this latest by EOD tomorrow (8th March 2022)

omshinde commented 2 years ago

Thanks @AlexanderJuestel, @crvernon for the update. I will match with @kanishkan91 and review the updates by March 8th EOD.

kanishkan91 commented 2 years ago

@AlexanderJuestel I ticked off the items on my list. But I had a couple of follow up questions so that I can close all issues that I opened.

Since the tests are all set up now, could you create a codecov badge for your repository , so I can check the the percentage of the code covered by tests? If you've not linked this repo to codecov, it is possible here -https://about.codecov.io/blog/python-code-coverage-using-github-actions-and-codecov/ . With this, you can ignore my comment on the Coverage.py.
Could you take a look at my comment about cleaning up the readme? I still think you can take out some of the images (where some of the links are broken) and maybe add an explicit link to the example.

Other than that, I think this is good to go. @crvernon Let me know what you think.

omshinde commented 2 years ago

@whedon generate pdf

editorialbot commented 2 years ago

My name is now @editorialbot

omshinde commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

omshinde commented 2 years ago

@AlexanderJuestel @crvernon I am ready with my final review and I have checked off the remaining items. The authors have done a great job to provide neat software and I congratulate them for their contributions. The updated documentation is comprehensive and detailed. Thank you to the authors for their efforts. From my side, I am happy to recommend the work to be published in JOSS.

Thanks, @crvernon for the follow-up and for the opportunity to review the manuscript.

kanishkan91 commented 2 years ago

@AlexanderJuestel I just checked the readme again and it looks good to me. I think you can take the comment about adding the codecov as a "suggested improvement". Overall, I think this good to be published. Thanks for all the responses!

@crvernon I recommend publishing.

crvernon commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

crvernon commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

AlexanderJuestel commented 2 years ago

@crvernon please let me know if there is anything I need to do prior to the publication

Cheers Alex

AlexanderJuestel commented 2 years ago

@crvernon any news from your side on the publication or is there any hold-up?

Cheers Alex

AlexanderJuestel commented 2 years ago

@omshinde @kanishkan91 Have you heard anything from @crvernon? Or is there anything that I still need to do with respect to the publication?

kanishkan91 commented 2 years ago

@AlexanderJuestel I haven't heard from @crvernon. But at this point of time, he may get back to you with any edits that he requires. You may be required to make some edits after the JOSS editor looks at it. But I think this is mostly done. Let's see what the reviewer says.

crvernon commented 2 years ago

@AlexanderJuestel apologies for the delay. I had a family emergency I had to tend to. I'll finalize this process early next week.

AlexanderJuestel commented 2 years ago

@crvernon I hope you and your family are doing better!

I just want to ask you to hold back the publishing of the paper for a little while as I need permission from my new institute to publish the work. It should only take a few days though. However, if you request any minor edits, I can for sure implement them already. Sorry for the inconvenience

crvernon commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

AlexanderJuestel commented 2 years ago

@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 commented 2 years ago

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

crvernon commented 2 years ago

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

crvernon commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

crvernon commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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 commented 2 years ago

@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:

[x] 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)
[x] 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.
[x] Please list the DOI of the archived version here

I can then move forward with accepting the submission.

AlexanderJuestel commented 2 years ago

Hi @crvernon,

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

crvernon commented 2 years ago

@editorialbot set v1.0.0 as version

editorialbot commented 2 years ago

Done! version is now v1.0.0

crvernon commented 2 years ago

@editorialbot set 10.5281/zenodo.6511767 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6511767

crvernon commented 2 years ago

@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 commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

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