editorialbot commented 6 months ago

Submitting author: !--author-handle-->@akinremisa@elbeejay<!--end-editor-- Reviewers: @paudetseis, @alistairboyce11 Archive: 10.5281/zenodo.13348322

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e7f2bc26984630e8b58ac80d9d96d85"><img src="https://joss.theoj.org/papers/4e7f2bc26984630e8b58ac80d9d96d85/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e7f2bc26984630e8b58ac80d9d96d85/status.svg)](https://joss.theoj.org/papers/4e7f2bc26984630e8b58ac80d9d96d85)

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

@paudetseis & @alistairboyce11, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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 ✨

Checklists

📝 Checklist for @paudetseis

📝 Checklist for @alistairboyce11

editorialbot commented 6 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (596.5 files/s, 159093.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              5              0              0           5613
Python                          33            787           2774           4519
Jupyter Notebook                12              0           1092            459
YAML                             3              9             12            134
Markdown                         2             48              0            105
JSON                             1             18              0             82
TeX                              1              0              0             73
TOML                             1              0              0              7
INI                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            59            862           3878          10995
-------------------------------------------------------------------------------

Commit count by author:

   141  akinremisa
     6  FadelI

editorialbot commented 6 months ago

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

OK DOIs

- 10.21105/joss.01808 is OK
- 10.1785/0120120290 is OK
- 10.1785/0220220288 is OK
- 10.1002/2014JB011610 is OK
- 10.1029/1999jb900322 is OK

MISSING DOIs

- None

INVALID DOIs

- underreview is INVALID

editorialbot commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 557

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 6 months ago

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

elbeejay commented 6 months ago

Hi @akinremisa, @paudetseis, and @alistairboyce11,

Thank you all for participating in the JOSS review process. At this time, I will be asking our generous reviewers to begin their reviews.

@paudetseis and @alistairboyce11, the instructions for making your checklist and conducting your reviews should be in the first comment of this issue, but please do not hesitate to reach out to me and I can definitely help you navigate this process. We prefer that larger comments be made as issues in the rfsed repository itself, and that this issue thread focus more on the JOSS process. This is to hopefully keep issues related to the content and code tied directly to the code repository itself. If possible, please link to this JOSS review issue in any rfsed repository issue you create, so that we have some connectivity there.

The JOSS review process can be 'conversational' in a way that is atypical for peer-reviewed journals. By this, we mean that you as the reviewer can have a direct dialog with the author as they respond to and make edits due to a reviewer comment you have made. We ask that you try to take a first pass and make comments within 6 weeks. If that is not possible it is not a problem, we just ask that you all try to keep the lines of communication open and communicate in this review thread if you're likely to miss the target deadline.

I will be asking the bot to send reminders in a few weeks to help keep this review from falling off of anyone's to-do list.

Thanks again! Jay

elbeejay commented 6 months ago

@editorialbot remind @paudetseis in three weeks

editorialbot commented 6 months ago

Reminder set for @paudetseis in three weeks

elbeejay commented 6 months ago

@editorialbot remind @alistairboyce11 in three weeks

editorialbot commented 6 months ago

Reminder set for @alistairboyce11 in three weeks

editorialbot commented 5 months ago

:wave: @paudetseis, please update us on how your review is going (this is an automated reminder).

editorialbot commented 5 months ago

:wave: @alistairboyce11, please update us on how your review is going (this is an automated reminder).

paudetseis commented 5 months ago

Review checklist for @paudetseis

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 https://github.com/akinremisa/rfsed?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@akinremisa) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

elbeejay commented 5 months ago

Thanks for providing a review and some thorough comments @paudetseis!

@alistairboyce11 please let me know if you have any questions about the process

alistairboyce11 commented 5 months ago

@editorialbot commands

editorialbot commented 5 months ago

Hello @alistairboyce11, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

alistairboyce11 commented 5 months ago

@editorialbot generate pdf

alistairboyce11 commented 5 months ago

Review checklist for @alistairboyce11

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 https://github.com/akinremisa/rfsed?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@akinremisa) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[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?

editorialbot commented 5 months ago

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

elbeejay commented 5 months ago

Thanks to both @paudetseis and @alistairboyce11 for opening up issues in the rfsed repository. @akinremisa you are welcome to provide responses to each in the respective issues and make changes to your repository as necessary. If you could comment here with some estimate of when you'll be able to read over and address the review comments I think that'd help both myself and our reviewers keep this on our schedules.

Thanks all!

akinremisa commented 5 months ago

Thank you @paudetseis and @alistairboyce11 for providing some reviews for the rfsed repository. @elbeejay I am able to respond to the reviews and make the necessary changes by 31 May at the latest.

akinremisa commented 4 months ago

@elbeejay I have responded to all the comments and also re-work the repository and fixed all the issues raised by the reviewers.

elbeejay commented 4 months ago

Thanks @akinremisa, when they get a chance @paudetseis will revisit the issue he opened (https://github.com/akinremisa/rfsed/issues/2) and @alistairboyce11 will revisit his review comments in (https://github.com/akinremisa/rfsed/issues/3) and provide additional comments and feedback as needed.

elbeejay commented 4 months ago

@alistairboyce11 from the review issue you opened up it seems like you were satisfied with the changes that were made in response to your comments. If that's the case, can you please update your reviewer checklist here when you get a chance? Thanks!

alistairboyce11 commented 3 months ago

Hi @akinremisa, hopefully that is all taken care of now. Thanks, Alistair

elbeejay commented 3 months ago

@akinremisa at this time I believe we are waiting on you to make some revisions or respond to the concerns in https://github.com/akinremisa/rfsed/issues/2, @paudetseis has indicated where he believes the revisions fall a bit short of what he was looking to see.

akinremisa commented 3 months ago

@paudetseis Thank you for your new comments and review. I am now working on fixing those. @elbeejay I am working on the revisions from Comment1 and will revert back

elbeejay commented 3 months ago

Checking in @akinremisa - do you have an estimate on when you'll be able to complete those revisions?

akinremisa commented 3 months ago

Hi @elbeejay. I have now completed the new revisions and will finalize it all later today and update the repository as required.

akinremisa commented 3 months ago

@elbeejay I have now responded to the new comments from @paudetseis and also provide details of the changes made in the Comment1

elbeejay commented 3 months ago

Great, thanks for the update.

elbeejay commented 2 months ago

Checking in here, @paudetseis it looks like @akinremisa has made revisions and replied to your comments in https://github.com/akinremisa/rfsed/issues/2. Do you feel your comments have been sufficiently addressed?

If so, if you could check off the last few items in your reviewer checklist above that'd be great.

elbeejay commented 2 months ago

@paudetseis - do you mind checking off the last few boxes in your reviewer checklist above? I understand that your comments were resolved in https://github.com/akinremisa/rfsed/issues/2, but we like to ask our reviewers to formally complete their checklists for posterity in the event we ever had to go back through JOSS reviews.

elbeejay commented 2 months ago

Big thank you to our reviewers, @paudetseis and @alistairboyce11. @akinremisa, we are nearing the end of the road here, I have just a few additional items to check and will require some information from you.

elbeejay commented 2 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

elbeejay commented 2 months ago

@akinremisa please let me know what the latest version number is, share the DOI of the archive once it is released on Zenodo, figshare, or an equivalent, and just check the metadata as indicated above. In the meantime I'll take care of those editor tasks and will let you know if I have any last comments or requests.

elbeejay commented 2 months ago

@editorialbot generate pdf

elbeejay commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- 10.1029/2023JB028393 is OK
- 10.21105/joss.01808 is OK
- 10.1785/0120120290 is OK
- 10.1002/2014JB011610 is OK
- 10.1029/1999jb900322 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 months ago

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

elbeejay commented 2 months ago

@akinremisa I'd ask that you consider:

increasing the font size on figure labels; the figures render correctly, but the labels are a bit tough to read without zooming in quite a bit on the PDF
Line 20: replace "derives" with the singular "derive"

akinremisa commented 2 months ago

@akinremisa I'd ask that you consider:

increasing the font size on figure labels; the figures render correctly, but the labels are a bit tough to read without zooming in quite a bit on the PDF

Line 20: replace "derives" with the singular "derive"

@elbeejay Thank you for your suggested edits. I have implemented these suggestions in the manuscript.

akinremisa commented 2 months ago

@akinremisa please let me know what the latest version number is, share the DOI of the archive once it is released on Zenodo, figshare, or an equivalent, and just check the metadata as indicated above. In the meantime I'll take care of those editor tasks and will let you know if I have any last comments or requests.

@elbeejay

The latest version of the software is 1.0.0

I have also uploaded this latest version to Zenodo.

Here is the Zenodo DOI: https://doi.org/10.5281/zenodo.13348322

akinremisa commented 2 months ago

@editorialbot set doi.org/10.5281/zenodo.13348322 as archive

editorialbot commented 2 months ago

I'm sorry @akinremisa, I'm afraid I can't do that. That's something only editors are allowed to do.

elbeejay commented 2 months ago

@editorialbot set v1.0.0 as version

editorialbot commented 2 months ago

Done! version is now v1.0.0

elbeejay commented 2 months ago

@editorialbot set 10.5281/zenodo.13348322 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.13348322

openjournals / joss-reviews

[REVIEW]: rfsed: Receiver function analysis and dealing with sediment effects #6612

Status

Reviewer instructions & questions

Checklists

Review checklist for @paudetseis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @alistairboyce11

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance