[REVIEW]: rf: Receiver function calculation in seismology #1808

whedon · 2019-10-14T13:06:55Z

Submitting author: @trichter (Tom Eulenfeld)
Repository: https://github.com/trichter/rf
Version: 0.9.1
Editor: @leouieda
Reviewers: @ThomasLecocq, @seisman
Archive: 10.5281/zenodo.3741366

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/47f72fe33d4defd396270bba1e0a8a58"><img src="https://joss.theoj.org/papers/47f72fe33d4defd396270bba1e0a8a58/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/47f72fe33d4defd396270bba1e0a8a58/status.svg)](https://joss.theoj.org/papers/47f72fe33d4defd396270bba1e0a8a58)

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

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

Make sure you're logged in to your GitHub account
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 @leouieda know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @ThomasLecocq

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 (@trichter) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @seisman

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 (@trichter) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 · 2019-10-14T13:06:58Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ThomasLecocq, @seisman it looks like you're currently assigned to review this paper 🎉.

⭐️ 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 · 2019-10-14T13:06:59Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-14T13:07:26Z

👉 Check article proof 📄 👈

leouieda · 2019-10-14T13:10:40Z

👋🏼 @trichter @seisman @ThomasLecocq this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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 openjournals/joss-reviews#1808 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 about 4 weeks. Please let me know if any of 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 here (@leouieda) or email me privately if you have any questions/concerns.

leouieda · 2019-10-30T12:05:55Z

👋 Hi @seisman @ThomasLecocq just checking in on the review progress. Are there any updates?

seisman · 2019-10-30T13:42:36Z

@leouieda I should be able to finish the review before this weekend.

leouieda · 2019-10-30T15:12:01Z

👍 thanks, @seisman! I appreciate the effort and quick feedback.

seisman · 2019-11-07T15:05:11Z

@leouieda I've finished my review and my comments have been addressed. The submission now looks good to me.

trichter · 2019-11-08T07:36:50Z

@seisman Thank you very much for the review!

leouieda · 2019-11-25T13:02:47Z

👋 Hi @ThomasLecocq just checking in to see how the review if progressing. Let me know if I can help in any way.

trichter · 2019-12-06T15:16:35Z

I updated the reference for the telewavesim package, which was recently published in JOSS.

trichter · 2019-12-06T15:16:51Z

@whedon generate pdf

whedon · 2019-12-06T15:16:54Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-06T15:17:20Z

👉 Check article proof 📄 👈

leouieda · 2019-12-06T16:06:05Z

Hi @trichter thanks for the update. Apologies for the delay in this submission. I'll see if we can speed things up after AGU next week.

leouieda · 2019-12-06T17:11:00Z

/ooo December 7 until December 17

ooo · 2019-12-06T17:11:01Z

👍 Marked @leouieda as OOO from Saturday, December 7th 2019 to Tuesday, December 17th 2019. 📆

leouieda · 2020-01-13T13:41:37Z

Waiting on a reply from @ThomasLecocq. If we don't hear back, I'll start looking for another reviewer (or probably just assign myself as a reviewer). Thanks for your patience @trichter 🙂

ThomasLecocq · 2020-01-20T07:16:18Z

wow guyz, sorry for this, noticed I disabled the github notifications a while ago... and @leouieda your emails went to spam... so I masterfully failed my assignment here...

Will do this week. Sorry about this.

leouieda · 2020-02-05T17:27:44Z

@ThomasLecocq any updates on this review?

trichter · 2020-04-06T07:59:56Z

@whedon generate pdf

whedon · 2020-04-06T08:00:29Z

👉 Check article proof 📄 👈

trichter · 2020-04-06T08:46:34Z

@leouieda I worked through your posted list:

Added your editorial suggestions and my orcid to the paper
Published a new version 0.9.1
Uploaded it to zenodo, the doi is 10.5281/zenodo.3741366

leouieda · 2020-04-06T11:05:28Z

@whedon set 0.9.1 as version

whedon · 2020-04-06T11:05:32Z

OK. 0.9.1 is the version.

leouieda · 2020-04-06T11:06:39Z

@whedon set 10.5281/zenodo.3741366 as archive

whedon · 2020-04-06T11:06:43Z

OK. 10.5281/zenodo.3741366 is the archive.

leouieda · 2020-04-06T11:07:35Z

@whedon generate pdf

whedon · 2020-04-06T11:08:08Z

👉 Check article proof 📄 👈

leouieda · 2020-04-06T11:10:24Z

@whedon accept

whedon · 2020-04-06T11:10:27Z

Attempting dry run of processing paper acceptance...

whedon · 2020-04-06T11:10:45Z

Reference check summary:

OK DOIs

- 10.1088/1749-4699/8/1/014003 is OK
- 10.1504/IJCSE.2009.029165 is OK
- 10.21105/joss.01818 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-04-06T11:10:55Z

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

Check final proof 👉 openjournals/joss-papers#1408

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1408, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

leouieda · 2020-04-06T11:13:57Z

@trichter thank you for implementing these final fixes. It's my pleasure to recommend your submission for publication in JOSS 🎉

A JOSS Associate Editor-in-Chief will stop by and do the final acceptance and publication (usually quick but please be patient given the current global crisis).

@seisman @ThomasLecocq thank for your reviews of this submission!

danielskatz · 2020-04-06T12:33:15Z

Thanks @leouieda - I'll take this now

danielskatz · 2020-04-06T12:38:31Z

@trichter - there are some small changes in trichter/rf#27

trichter · 2020-04-06T13:47:22Z

@danielskatz Thanks for these. I merged your branch.

trichter · 2020-04-06T13:48:07Z

@whedon generate pdf

whedon · 2020-04-06T13:48:39Z

👉 Check article proof 📄 👈

danielskatz · 2020-04-06T14:03:53Z

@whedon accept deposit=true

whedon · 2020-04-06T14:03:56Z

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

whedon · 2020-04-06T14:04:56Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-04-06T14:04:57Z

🚨🚨🚨 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 👉 openjournals/joss-papers#1409
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01808
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

danielskatz · 2020-04-06T14:08:27Z

Thanks to @ThomasLecocq & @seisman for reviewing, and @leouieda for editing!

Congratulations to @trichter!

whedon · 2020-04-06T14:08:43Z

🎉🎉🎉 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.01808/status.svg)](https://doi.org/10.21105/joss.01808)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01808">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01808/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01808/status.svg
   :target: https://doi.org/10.21105/joss.01808

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

whedon added the review label Oct 14, 2019

whedon assigned leouieda Oct 14, 2019

whedon mentioned this issue Oct 14, 2019

[PRE REVIEW]: rf: Receiver function calculation in seismology #1795

Closed

whedon assigned seisman Oct 15, 2019

seisman mentioned this issue Oct 29, 2019

[JOSS review] Errors when install toeplitz #18

Closed

This was referenced Nov 4, 2019

[JOSS review] Mention the RTZ coordinate system in the method section trichter/rf#19

Closed

[JOSS review] Add the links of tutorial notebooks to the documentation trichter/rf#20

Closed

[JOSS] The second notebook example doesn't work well trichter/rf#21

Closed

whedon assigned ThomasLecocq Jan 21, 2020

ThomasLecocq mentioned this issue Feb 28, 2020

Review - windows compatibility made easier :) #24

Merged

whedon added the recommend-accept label Apr 6, 2020

danielskatz mentioned this issue Apr 6, 2020

small fixes in paper #27

Merged

whedon added accepted published labels Apr 6, 2020

danielskatz closed this Apr 6, 2020

openjournals / joss-reviews

Sponsor openjournals/joss-reviews

Join GitHub today

[REVIEW]: rf: Receiver function calculation in seismology #1808

[REVIEW]: rf: Receiver function calculation in seismology #1808

Comments

whedon commented Oct 14, 2019 • edited

Status

Reviewer instructions & questions

Review checklist for @ThomasLecocq

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @seisman

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

This comment has been minimized.

whedon commented Oct 14, 2019

This comment has been minimized.

whedon commented Oct 14, 2019

This comment has been minimized.

whedon commented Oct 14, 2019

This comment has been minimized.

leouieda commented Oct 14, 2019

This comment has been minimized.

leouieda commented Oct 30, 2019

This comment has been minimized.

seisman commented Oct 30, 2019

This comment has been minimized.

leouieda commented Oct 30, 2019

This comment has been minimized.

seisman commented Nov 7, 2019

This comment has been minimized.

trichter commented Nov 8, 2019

This comment has been minimized.

leouieda commented Nov 25, 2019

This comment has been minimized.

trichter commented Dec 6, 2019

This comment has been minimized.

trichter commented Dec 6, 2019

This comment has been minimized.

whedon commented Dec 6, 2019

This comment has been minimized.

whedon commented Dec 6, 2019

This comment has been minimized.

leouieda commented Dec 6, 2019

This comment has been minimized.

leouieda commented Dec 6, 2019

This comment has been minimized.

ooo bot commented Dec 6, 2019

This comment has been minimized.

leouieda commented Jan 13, 2020

This comment has been minimized.

ThomasLecocq commented Jan 20, 2020

This comment has been minimized.

leouieda commented Feb 5, 2020

This comment has been minimized.

trichter commented Apr 6, 2020

This comment has been minimized.

whedon commented Apr 6, 2020

This comment has been minimized.

trichter commented Apr 6, 2020 • edited

This comment has been minimized.

leouieda commented Apr 6, 2020

This comment has been minimized.

whedon commented Apr 6, 2020

This comment has been minimized.

leouieda commented Apr 6, 2020

This comment has been minimized.

whedon commented Apr 6, 2020

This comment has been minimized.

leouieda commented Apr 6, 2020

This comment has been minimized.

whedon commented Oct 14, 2019 •

edited

trichter commented Apr 6, 2020 •

edited