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

whedon commented 3 years ago

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

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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

@abhishekvp & @omshinde & @arbennett, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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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

[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 (@ebocher) 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 @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

[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 (@ebocher) 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?

ebocher commented 3 years ago

@elbeejay

Can you make a tagged release of the current codebase? 27 commits have been made since 0.0.1 and I think at least 1 modified the source code.

The commits are related to the doc not the code. I have compiled a new version of the doc with the release 0.0.1 that includes the commits. So I think it's not necessary to upgrade geoclimate to 0.0.2

ebocher commented 3 years ago

@arfon

I realize this is extra work for you all but our current document-production toolchain requires a DOI for the archive.

Don't worry about that. We will used zenodo. Thanks to offer JOSS the community.

ebocher commented 3 years ago

@arfon This done on zenodo ;-) https://zenodo.org/record/5534680 and the DOI : 10.5281/zenodo.5534680

elbeejay commented 3 years ago

@whedon generate pdf

elbeejay commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

elbeejay commented 3 years ago

@whedon set 0.0.1 as version

whedon commented 3 years ago

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

whedon commented 3 years ago

OK. 0.0.1 is the version.

elbeejay commented 3 years ago

@whedon set 10.5281/zenodo.5534680 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5534680 is the archive.

elbeejay commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

elbeejay commented 3 years ago

@ebocher and co-authors: I've recommended that your submission be accepted and published at this time. The final steps will be handled by one of the EiCs. Many thanks to @omshinde, @abhishekvp, and @arbennett for their thoughtful reviews.

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2632

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2632, 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 commented 3 years ago

FYI - I changed the title as there should never be a space before a ":" in English text, unlike some programming languages.

danielskatz commented 3 years ago

@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

danielskatz commented 3 years ago

@whedon generate pdf (just checking to make sure the space is removed in the title of the paper too)

danielskatz commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

whedon commented 3 years ago

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

ebocher commented 3 years ago

@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 commented 3 years ago

@danielskatz Title fixed in the paper zenodo title updated

danielskatz commented 3 years ago

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

ebocher commented 3 years ago

@danielskatz Thanks a lot. Merged

danielskatz commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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 commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2633

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

danielskatz commented 3 years ago

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 commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years 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/2634
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03541
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

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

ebocher commented 3 years ago

Dear JOSS team, dear whedon genius,

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

danielskatz commented 3 years ago

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

danielskatz commented 3 years ago

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 commented 3 years 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.03541/status.svg)](https://doi.org/10.21105/joss.03541)

HTML:
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  <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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