[REVIEW]: GeoClimate: a Geospatial processing toolbox for environmental and climate studies

[whedon]

Submitting author: @ebocher (Erwan Bocher)
Repository: https://github.com/orbisgis/geoclimate/
Version: 0.0.1
Editor: @elbeejay
Reviewer: @abhishekvp, @omshinde, @arbennett
Archive: 10.5281/zenodo.5534680

⚠️ 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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2b216ea704e5ee9d61a8208463c17ce1"><img src="https://joss.theoj.org/papers/2b216ea704e5ee9d61a8208463c17ce1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2b216ea704e5ee9d61a8208463c17ce1/status.svg)](https://joss.theoj.org/papers/2b216ea704e5ee9d61a8208463c17ce1)

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

@abhishekvp & @omshinde & @arbennett, 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 @elbeejay 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 @abhishekvp

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 (@ebocher) 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 @omshinde

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 (@ebocher) 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 @arbennett

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 (@ebocher) 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. @abhishekvp, @omshinde, @arbennett 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.

⭐ Important ⭐

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:

2. 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

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1023/A:1002463829265 is OK
- 10.1175/BAMS-D-11-00019.1 is OK
- 10.1016/j.uclim.2018.01.008 is OK
- 10.1016/j.uclim.2019.100536 is OK
- 10.1016/j.buildenv.2017.08.009 is OK
- 10.3389/fenvs.2021.637455 is OK
- 10.1016/j.envsoft.2017.09.020 is OK
- 10.1016/j.uclim.2015.04.001 is OK
- 10.1002/met.29 is OK
- 10.1007/s00704-015-1405-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Wordcount for paper.md is 2368

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.28 s (74.8 files/s, 118855.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              5             14             16          78777
SVG                              1              1              1          44890
Groovy                          37           1848           3232          15668
JSON                            32              5              0           4734
Scheme                           3              1              0            799
Maven                            5             29              7            761
SQL                              6            196            297            702
Markdown                         4             84              0            219
TeX                              1             11              0            147
YAML                             2              4              4             38
-------------------------------------------------------------------------------
SUM:                            96           2193           3557         146735
-------------------------------------------------------------------------------


Statistical information for the repository '2f3167a49ed43e063d1d57ef' was
gathered on 2021/07/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Bocher                           2             4              4            0.12
Elisabeth Le Saux                2           626            409           15.44
Palominos Sylvain                4             8             50            0.87
ebocher                         25          1389           1029           36.07
gpetit                          22          1652            343           29.76
jeremy                           1            22             22            0.66
jeremy-b                        50           604            441           15.59
nahtanojoal                      4            94              6            1.49

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Bocher                      368         9200.0          7.1                3.53
gpetit                      623           37.7         24.7               44.78
jeremy-b                    202           33.4         17.8                2.48
nahtanojoal                   2            2.1         26.5                0.00

[whedon]

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

[elbeejay]

@abhishekvp, @omshinde, and @arbennett, thanks for agreeing to review this submission to JOSS. We are currently asking reviewers to try and complete their reviews in 6 weeks.

The JOSS review process is entirely open and transparent, and takes place on GitHub. Review comments can be made as issues in the GeoClimate repository, please link this review issue when doing so (paste https://github.com/openjournals/joss-reviews/issues/3541 into the issue).

For reference, here are links to the JOSS documentation that may be helpful as you conduct your reviews:

• JOSS Review Criteria
• JOSS Review Checklist

Please feel free to ping me (@elbeejay) if you have any questions/concerns. Thanks again for agreeing to review for JOSS.

[whedon]

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

[whedon]

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

[whedon]

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

[elbeejay]

👋 Hello @abhishekvp @arbennett @omshinde we're at the halfway point for this review so I wanted to just check in with you all. Please feel free to reach out if you have any questions about the JOSS review process.

[omshinde]

Hi @elbeejay
Thanks for the reminder. I have started preliminary review locally in my system but I am afraid that I am not able to update my checklist. Maybe because I am not assigned or added as collaborator. Please check it once so that I can update the checklist too (I hope I am not missing anything). Thanks!

[elbeejay]

@whedon re-invite @omshinde as reviewer

[whedon]

The reviewer already has a pending invite.

@omshinde please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[elbeejay]

Hopefully the new invitation to review will give you access to the checklist @omshinde 🤞.

[omshinde]

Thanks for the follow-up and really sorry for missing out on accepting the invitation. I tried accepting it now but it says that the invitation was revoked or I am not logged in with correct account (which I double checked and is not the case).

[elbeejay]

Thanks for following up @omshinde, if you cannot access the checklist please continue to perform your review anyway. You can copy the checklist items and make a comment in this issue if you'd like to have a way to keep track. Otherwise just open issues if/as necessary in the project repository, and let me know here when you've completed your review. Thanks!

[omshinde]

Review checklist for @omshinde

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 (@ebocher) 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?

[elbeejay]

👋 @abhishekvp @arbennett @omshinde just checking in here now that we are 5 weeks into the review period. Please let me know if you will be unable to finish your review by September 6th.

As always, ping me with any questions about the JOSS process.

[omshinde]

Hi @elbeejay
Thanks for the reminder. I am on track with the review timeline and would submit it before Sep 6th.

[arbennett]

Hey @elbeejay I am also on track with the review and should be able to finish up in the next couple days. Thanks for checking in!

[omshinde]

@elbeejay @ebocher

Review 1:
Thanks to the authors for their contributions. Please find my queries and suggestions below regarding the submission - "GeoClimate: a geospatial processing toolbox for environmental and climate studies".

Working Environment:
OS - Ubuntu 20.04.2 LTS

Functionality

Query: The download link as mentioned on https://github.com/orbisgis/geoclimate/wiki/Download#geoclimate-for-command-line-interface for the Geoclimate.jar redirects to file not found for me. Could you please recheck and confirm? I hope I am not missing anything here. Thanks!

I will continue my review for functionality and documentation after receiving response in this regard.

Software Paper

References

1. Minor Suggestion - The authors could consider citing the UMEP manual instead of putting the link as footnote in the Software paper.
   1.1 (Please refer: https://umep-docs.readthedocs.io/en/latest/Introduction.html#umep-how-to-cite)

   Lindberg F, Grimmond CSB, A Gabey, L Jarvi, CW Kent, N Krave, T Sun, N Wallenberg, HC Ward (2019) Urban Multi-scale Environmental Predictor (UMEP) Manual. https://umep-docs.readthedocs.io/ University of Reading UK, University of Gothenburg Sweden, SIMS China

[ebocher]

@omshinde
Thank you for pointing out this error. The page has been updated and the link is now pointing to the releases page.

[danielskatz]

@whedon generate pdf

[whedon]

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

[whedon]

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

[ebocher]

@danielskatz

@ebocher - please change the metadata on the zenodo deposit to match the title and authors of the paper, and let us know when this is done

Do you want the same name as in the paper ?

[ebocher]

@danielskatz
Title fixed in the paper
zenodo title updated

[danielskatz]

@ebocher - I've suggested some minor changes in the paper in orbisgis/geoclimate#635 - please merge this or let me know what you disagree with

[ebocher]

@danielskatz
Thanks a lot. Merged

[danielskatz]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1023/A:1002463829265 is OK
- 10.1175/BAMS-D-11-00019.1 is OK
- 10.1016/j.uclim.2018.01.008 is OK
- 10.1016/j.uclim.2019.100536 is OK
- 10.1016/j.buildenv.2017.08.009 is OK
- 10.3389/fenvs.2021.637455 is OK
- 10.1016/j.envsoft.2017.09.020 is OK
- 10.1016/j.uclim.2015.04.001 is OK
- 10.1002/met.29 is OK
- 10.1007/s00704-015-1405-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2633

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2633, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[danielskatz]

I just noticed that @arbennett didn't check the box for

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?

@arbennett - can you check this box, or let us know if there was a problem?

[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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03541 joss-papers#2634
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03541
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...

[danielskatz]

I'm going to hold this issue open until the last checkbox item from @arbennett is resolved.

[ebocher]

Dear JOSS team, dear whedon genius,

Thanks a lot to offer this journal to the community and drive us during the reviewing steps.

[danielskatz]

Ok, thanks to @arbennett for coming back and fixing the last checkbox - we're all done now!!

[danielskatz]

Congratulations to @ebocher (Erwan Bocher) and co-authors!!

And thanks to @abhishekvp, @omshinde, and @arbennett for reviewing, and @elbeejay for editing!
We couldn't do this without you!!

[whedon]

🎉🎉🎉 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.03541/status.svg)](https://doi.org/10.21105/joss.03541)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03541">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03541/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03541/status.svg
   :target: https://doi.org/10.21105/joss.03541

This is how it will look in your documentation:

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