[REVIEW]: sandpyper: A Python package for UAV-SfM beach volumetric and behavioural analysis

whedon commented 3 years ago

Submitting author: @npucino (Nicolas Pucino) Repository: https://github.com/npucino/sandpyper Version: v1.3.3 Editor: @crvernon Reviewer: @dbuscombe-usgs, @chrisleaman Archive: 10.5281/zenodo.5565487

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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

@dbuscombe-usgs & @chrisleaman, 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 @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 @dbuscombe-usgs

✨ 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 (@npucino) 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 @chrisleaman

✨ 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 (@npucino) 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?

npucino commented 2 years ago

@crvernon All done!. Thanks for the suggestion!

crvernon commented 2 years ago

@whedon generate pdf

whedon 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

@npucino - 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 master 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 (make sure the list is correct and people who only made a small fix are not on it). 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.

npucino commented 2 years ago

@crvernon all done!

here is the DOI: 10.5281/zenodo.5563134 Thanks!

crvernon commented 2 years ago

@npucino - I took a look at the Zenodo archive you referred to (https://zenodo.org/record/5563134#.YWVnNBDML6A) and it doesn't seem to have to code accessible. Did you link Zenodo with the sandpyper repository before you conducted the release? If not, could you please do so and re-release to make sure that all of the files are included in the record? If so, something is not processing correctly. I will be happy to help you troubleshoot if you have any questions.

Also, please change the name of the GitHub release for the final version to the title of the JOSS paper the way you did for the Zenodo record.

Thanks!

npucino commented 2 years ago

@crvernon oh no, I uploaded manually the files into Zenodo. I selected everything was inside my sandpyper repo but did't realise that folders (where the actual code is) were not included.

Now that you mentioned the Github-Zenodo link I discovered that feature, which is awesome. I link, re-release with JOSS paper title and let you know asap! I do it now,

Thanks and sorry for this.

npucino commented 2 years ago

@crvernon I love this Zenodo feature.

I hope I did it right but it should be fine now.

Here is the link to the Zenodo archive: https://zenodo.org/record/5565487#.YWYPHRpBwUE

DOI: 10.5281/zenodo.5565487

Thanks!

crvernon commented 2 years ago

@whedon set v1.3.3 as version

whedon commented 2 years ago

OK. v1.3.3 is the version.

crvernon commented 2 years ago

@whedon set 10.5281/zenodo.5565487 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5565487 is the archive.

crvernon commented 2 years ago

🎉 @npucino thanks for putting together a really nice software product! Thanks to @dbuscombe-usgs and @chrisleaman 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

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1111/0031-868x.00152 is OK
- 10.1371/journal.pone.0118571 is OK
- 10.1890/10-1510.1 is OK
- 10.1038/s41598-021-83477-6 is OK
- 10.1016/j.earscirev.2017.04.011 is OK
- 10.1016/j.ecolecon.2006.10.022 is OK
- 10.1016/j.ocecoaman.2018.01.001 is OK
- 10.1016/j.isprsjprs.2015.02.009 is OK
- 10.21105/joss.01890 is OK
- 10.1038/sdata.2016.24 is OK
- 10.3390/data4020073 is OK
- 10.3390/ijgi8060267 is OK
- 10.1016/j.geomorph.2016.02.025 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 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/2667

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2667, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

npucino commented 2 years ago

🎉 @npucino thanks for putting together a really nice software product! Thanks to @dbuscombe-usgs and @chrisleaman 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.

Thank you @crvernon for your overview and guidance and thank you @dbuscombe-usgs and @chrisleaman for helping me making this package a much better product than before!

I learned many important new things and best practices. I also set new goals to Sandpyper roadmap to make it even better in the near future. I would recommend to go through this process to anyone involved in Open Source dev, especially at early stage coders like myself!

Thanks again everyone! Best Regards,

Nick

npucino commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

I'm sorry @npucino, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

npucino commented 2 years ago

I'm sorry @npucino, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

Ops, I thought I had to check that! cheers

arfon commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 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/2668
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03666
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 2 years ago

@dbuscombe-usgs, @chrisleaman – many thanks for your reviews here and to @crvernon 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 ✨

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

whedon commented 2 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:

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reStructuredText:
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