[REVIEW]: rsudp: A Python package for real-time seismic monitoring with Raspberry Shake instruments

[whedon]

Submitting author: @iannesbitt (Ian Nesbitt)
Repository: https://github.com/raspishake/rsudp
Version: 1.1.0
Editor: @jedbrown
Reviewers: @fwalter, @calum-chamberlain
Archive: 10.5281/zenodo.5771026

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/11e2afeb2d45da49b4092e8311c8f8a4/status.svg)](https://joss.theoj.org/papers/11e2afeb2d45da49b4092e8311c8f8a4)

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

@calum-chamberlain and @fwalter, 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 @jedbrown 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 @calum-chamberlain

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 (@iannesbitt) 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 @fwalter

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 (@iannesbitt) 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?

[whedon]

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

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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:

OK DOIs

- 10.1785/0220180251 is OK
- 10.1785/0220190211 is OK
- 10.3389/feart.2020.00009 is OK
- 10.3389/feart.2020.00073 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1785/gssrl.81.3.530 is OK
- 10.4401/ag-4838 is OK
- 10.1088/1749-4699/8/1/014003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[jedbrown]

@eileenrmartin 👋 Welcome to JOSS and thanks for agreeing to review!

The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the rsudp repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #2565 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

[labarba]

hi 👋 @eileenrmartin – I'm the associate EiC on rotation this week. I notice this review has no movement in several weeks. Could we have an update from you about your availability to complete the review? Thanks!

[iannesbitt]

note to reviewers, here is a potentially relevant recent citation that uses RS that might be good to include among the first few references cited:

https://science.sciencemag.org/content/369/6509/1338.abstract

[jedbrown]

@whedon add @fwalter as reviewer

[whedon]

OK, @fwalter is now a reviewer

[jedbrown]

@fwalter (Fabian Walter) 👋 Welcome to JOSS and thanks for agreeing to review!

The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the rsudp repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #2565 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

[fwalter]

Dear Jed, I have reviewed this software package and would now like to submit my report. Do I understand correctly that this should be done as an issue on the repository: https://github.com/raspishake/rsudp/issues Also, where can I fill out the checklist, which is mentioned here: https://joss.readthedocs.io/en/latest/review_checklist.html I tried to accept the invitation by whedon, but this seems to have expired. Is that a problem? In general, this software package compiles and functions well, but it seems to be mostly (perhaps only) useful for educational purposes. For research or monitoring purposes one has to include custom modules, which I found tedious, especially when the user is not highly fluent in python. Thanks for your help! Fabian. Am Mi., 18. Nov. 2020 um 02:17 Uhr schrieb Jed Brown < [email protected]>:

…

@fwalter <https://github.com/fwalter> (Fabian Walter) 👋 Welcome to JOSS and thanks for agreeing to review! The comments from @whedon <https://github.com/whedon> above outline the review process, which takes place in this thread (possibly with issues filed in the rsudp repository <https://github.com/raspishake/rsudp/>). I'll be watching this thread if you have any questions. The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #2565 <#2565> so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package. We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time. Please feel free to ping me ***@***.*** <https://github.com/jedbrown>) if you have any questions/concerns. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2565 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADC2IN53Q3FSUPMDTIBKK3DSQMODFANCNFSM4P7RIADA> .

-- Fabian Walter ETH Zurich Laboratory of Hydraulics, Hydrology and Glaciology V. Wasserbau, Hydrologie u. Glaz. HIA D 56.1 Hönggerbergring 26 8093 Zürich Phone: +41 44 632 4162 http://n.ethz.ch/~fwalter/

[jedbrown]

@whedon re-invite @fwalter as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[jedbrown]

@fwalter Thanks! When you accept that fresh invitation, you should be able to click in the checkboxes.

Indeed, general comments can go directly in this thread, but specific "to do" items should be filed as issues in https://github.com/raspishake/rsudp/issues. They'll be automatically linked from here if you mention this issue (https://github.com/openjournals/joss-reviews/issues/2565).

[jedbrown]

Hi, @eileenrmartin 👋 Is there anything we can do to facilitate your review?

[jedbrown]

@whedon generate pdf

[whedon]

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

[jedbrown]

Looks good. @iannesbitt Could you please tag a release (annotated tag preferred) and archive on Zenodo or similar? Please make sure the author list matches this submission and report the DOI back here.

[iannesbitt]

Hi @jedbrown, here is the tag and DOI record.

Release: 1.1.0
Zenodo: https://zenodo.org/record/5771026
doi: 10.5281/zenodo.5771026

[jedbrown]

@whedon set 1.1.0 as version

[whedon]

OK. 1.1.0 is the version.

[jedbrown]

@whedon set 10.5281/zenodo.5771026 as archive

[whedon]

OK. 10.5281/zenodo.5771026 is the archive.

[jedbrown]

@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

- 10.1785/0220180251 is OK
- 10.1785/0220190211 is OK
- 10.3389/feart.2020.00009 is OK
- 10.3389/feart.2020.00073 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1785/gssrl.81.3.530 is OK
- 10.4401/ag-4838 is OK
- 10.1088/1749-4699/8/1/014003 is OK
- 10.1126/science.abd2438 is OK
- 10.5066/P93A9MWK is OK
- 10.1785/0220200483 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#2809

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2809, 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...

[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.02565 joss-papers#2810
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02565
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]

Congratulations to @iannesbitt (Ian Nesbitt) and co-authors!!

And thanks to @fwalter and @calum-chamberlain for reviewing, and @jedbrown 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.02565/status.svg)](https://doi.org/10.21105/joss.02565)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02565">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02565/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02565/status.svg
   :target: https://doi.org/10.21105/joss.02565

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[iannesbitt]

Thank you all for your contributions, and sorry it took so long!

[calum-chamberlain]

Good job all, and apologies again for my part in the hold-ups. Thank you for your patience @iannesbitt

[jedbrown]

Indeed, thank you all for your important work and patience.

[iannesbitt]

@jedbrown a reader pointed out a small typographical error in the references: "Geolgical" should be "Geological". Wondering if it's too late to change now. I've made the necessary edit to the .bib file.

[jedbrown]

@danielskatz Is this something you can do or only Arfon? It's quite minor.

[danielskatz]

The best thing is to ping @openjournals/dev for things like this - it's not me :)