[REVIEW]: lidar: A Python package for delineating nested surface depressions from digital elevation data #2965

whedon · 2021-01-15T20:14:09Z

Submitting author: @giswqs (Qiusheng Wu)
Repository: https://github.com/giswqs/lidar
Version: 0.6.1
Editor: @kbarnhart
Reviewers: @laijingtao, @cheginit, @amanaster2
Archive: 10.5281/zenodo.4571011

⚠️ JOSS reduced service mode ⚠️

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@laijingtao & @cheginit & @amanaster2, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @laijingtao

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 (@giswqs) 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: Do the authors clearly state 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 @cheginit

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 (@giswqs) 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: Do the authors clearly state 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 @amanaster2

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 (@giswqs) 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: Do the authors clearly state 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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-01-15T20:14:16Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @laijingtao, @cheginit, @amanaster2 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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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 · 2021-01-15T20:14:48Z

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

OK DOIs

- 10.1016/j.cageo.2005.11.002 is OK
- 10.1016/j.geomorph.2016.05.006 is OK
- 10.1007/s13157-015-0731-6 is OK
- 10.1080/13658816.2015.1038719 is OK
- 10.1111/1752-1688.12689 is OK
- 10.1080/13658810500433453 is OK
- 10.1080/13658816.2014.975715 is OK
- 10.1002/hyp.10648 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.7287/peerj.preprints.27099v1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-01-15T20:15:29Z

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

kbarnhart · 2021-01-15T20:15:56Z

It looks like I accidentally unassigned the reviewers so I'm going to re-add them with whedon.

kbarnhart · 2021-01-15T20:16:34Z

@whedon add @laijingtao as reviewer

whedon · 2021-01-15T20:16:40Z

OK, @laijingtao is now a reviewer

kbarnhart · 2021-01-15T20:18:00Z

@whedon add @cheginit as reviewer

whedon · 2021-01-15T20:18:06Z

OK, @cheginit is now a reviewer

kbarnhart · 2021-01-15T20:18:21Z

@whedon add @amanaster2 as reviewer

whedon · 2021-01-15T20:18:28Z

OK, @amanaster2 is now a reviewer

laijingtao · 2021-01-22T05:26:36Z

Hi Katy @kbarnhart, it seems that I can't click the checkbox and my names is not listed as one of the assignees. Also, I clicked the link for accepting invitation but it said that it could find the invitation. This is my first time reviewing for joss. Could you help me figure out what could be wrong?

kbarnhart · 2021-01-22T15:28:46Z

@whedon re-invite @laijingtao as reviewer

whedon · 2021-03-01T18:54:50Z

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

kbarnhart · 2021-03-01T19:08:17Z

@giswqs please fix the .bib file so John B Lindsay and J B Lindsay are not disambiguated. This occurs when the author names are different. If you make all of them "Lindsay, J B" it should fix it.

Once you have made that fix and verified that it builds correctly as a PDF, please do the following:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) 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.
Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

giswqs · 2021-03-01T20:06:17Z

@whedon generate pdf

whedon · 2021-03-01T20:07:05Z

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

giswqs · 2021-03-01T20:21:34Z

@kbarnhart I have fixed the paper.bib file. See the article proof. Thanks.

Tagged version: v0.6.1
Zenodo link: https://doi.org/10.5281/zenodo.4571011
DOI: 10.5281/zenodo.4571011

kbarnhart · 2021-03-02T19:45:41Z

@whedon set 0.6.1 as version

whedon · 2021-03-02T19:45:45Z

OK. 0.6.1 is the version.

kbarnhart · 2021-03-02T19:45:57Z

@whedon set 10.5281/zenodo.4571011 as archive

whedon · 2021-03-02T19:46:01Z

OK. 10.5281/zenodo.4571011 is the archive.

kbarnhart · 2021-03-02T19:46:16Z

@whedon accept

whedon · 2021-03-02T19:46:19Z

Attempting dry run of processing paper acceptance...

whedon · 2021-03-02T19:46:55Z

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

OK DOIs

- 10.1016/j.cageo.2005.11.002 is OK
- 10.1016/j.geomorph.2016.05.006 is OK
- 10.1007/s13157-015-0731-6 is OK
- 10.1080/13658816.2015.1038719 is OK
- 10.1111/1752-1688.12689 is OK
- 10.1080/13658810500433453 is OK
- 10.1080/13658816.2014.975715 is OK
- 10.1002/hyp.10648 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.7287/peerj.preprints.27099v1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kbarnhart · 2021-03-02T19:47:42Z

@giswqs I've now recommended that this submission be accepted and published. One of the JOSS EiC's @openjournals/joss-eics will manage final publication steps.

Thanks to @laijingtao @cheginit and @amanaster2 for contributing reviews.

whedon · 2021-03-02T19:47:48Z

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

Check final proof 👉 openjournals/joss-papers#2128

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2128, 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 · 2021-03-02T20:22:16Z

@whedon accept deposit=true

whedon · 2021-03-02T20:22:19Z

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

whedon · 2021-03-02T20:24:04Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-03-02T20:24:05Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.02965 joss-papers#2129
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02965
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2021-03-02T20:30:55Z

Congratulations to @giswqs (Qiusheng Wu)!!

And thanks to @laijingtao, @cheginit, and @amanaster2 for reviewing, and @kbarnhart for editing!

whedon · 2021-03-02T20:31:00Z

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

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.02965/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02965/status.svg
   :target: https://doi.org/10.21105/joss.02965

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giswqs · 2021-03-02T21:19:32Z

@kbarnhart Thank you very much for handling my submission. Much appreciated.

@laijingtao @cheginit and @amanaster2 Thank you all for your constructive comments that greatly improved the package.

whedon added Makefile Python review TeX labels Jan 15, 2021

whedon assigned kbarnhart Jan 15, 2021

whedon mentioned this issue Jan 15, 2021

[PRE REVIEW]: lidar: A Python package for terrain and hydrological analysis using digital elevation models #2896

Closed

whedon assigned cheginit and kbarnhart and unassigned kbarnhart Jan 15, 2021

whedon assigned cheginit and kbarnhart and unassigned kbarnhart and cheginit Jan 15, 2021

whedon assigned amanaster2 Jan 16, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 2, 2021

whedon added accepted published Papers published in JOSS labels Mar 2, 2021

danielskatz closed this as completed Mar 2, 2021

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[REVIEW]: lidar: A Python package for delineating nested surface depressions from digital elevation data #2965

[REVIEW]: lidar: A Python package for delineating nested surface depressions from digital elevation data #2965

whedon commented Jan 15, 2021 •

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[REVIEW]: lidar: A Python package for delineating nested surface depressions from digital elevation data #2965

[REVIEW]: lidar: A Python package for delineating nested surface depressions from digital elevation data #2965

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whedon commented Jan 15, 2021 • edited Loading

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Reviewer instructions & questions

Review checklist for @laijingtao

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @cheginit

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @amanaster2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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