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[REVIEW]: Telewavesim: Python software for teleseismic body wave modeling #1818

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whedon opened this issue Oct 18, 2019 · 70 comments
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@whedon whedon commented Oct 18, 2019

Submitting author: @paudetseis (Pascal Audet)
Repository: https://github.com/paudetseis/Telewavesim
Version: v0.2.0
Editor: @kbarnhart
Reviewer: @andreww, @seisman, @brmather
Archive: 10.5281/zenodo.3551258

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/dd49a1b3a0b51840e30996d5a3ffdb43"><img src="https://joss.theoj.org/papers/dd49a1b3a0b51840e30996d5a3ffdb43/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dd49a1b3a0b51840e30996d5a3ffdb43/status.svg)](https://joss.theoj.org/papers/dd49a1b3a0b51840e30996d5a3ffdb43)

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

@andreww & @seisman & @brmather, 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 @kbarnhart know.

Please try and complete your review in the next two weeks

Review checklist for @andreww

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

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 (@paudetseis) 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

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 (@paudetseis) 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 @brmather

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

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 (@paudetseis) 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?
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@whedon whedon commented Oct 18, 2019

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

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

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  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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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
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@whedon whedon commented Oct 18, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Oct 18, 2019

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@kbarnhart kbarnhart commented Oct 24, 2019

@whedon remind @andreww in one week

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@whedon whedon commented Oct 24, 2019

Reminder set for @andreww in one week

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@kbarnhart kbarnhart commented Oct 24, 2019

@whedon remind @seisman in one week

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@whedon whedon commented Oct 24, 2019

Reminder set for @seisman in one week

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@kbarnhart kbarnhart commented Oct 24, 2019

@whedon remind @brmather in one week

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@whedon whedon commented Oct 24, 2019

Reminder set for @brmather in one week

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@danielskatz danielskatz commented Oct 24, 2019

@kbarnhart - FYI, @whedon only takes one command at a time, and it has to be the first content in the comment

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@kbarnhart kbarnhart commented Oct 24, 2019

@danielskatz thanks for the the @whedon info! 👍 I've edited the comment to split up the reminders.

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@paudetseis paudetseis commented Oct 24, 2019

Question to @kbarnhart and reviewers: I see new issues on the GH repo from @seisman and making corrections as they come. Should I push them now or wait for potentially more comments from reviewers?

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@kbarnhart kbarnhart commented Oct 25, 2019

@paudetseis - it’s up to you if you want to wait for all the reviews, or start addressing the issues as they arrive.

It’s definitely good to do as @seisman has done and make sure to to link the reviews in the repository. That way the substantive review comments can be in the in-repository issues, but this issue can have a record of the the status.

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@whedon whedon commented Nov 23, 2019

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@kbarnhart kbarnhart commented Nov 23, 2019

@whedon set v0.2.0 as version

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@whedon whedon commented Nov 23, 2019

OK. v0.2.0 is the version.

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@kbarnhart kbarnhart commented Nov 23, 2019

@paudetseis I found that the DOI you mentioned here is not resolved (https://doi.org/10.5281/zenodo.203551250).

Following the link on the readme I find: http://doi.org/10.5281/zenodo.3551258

Can you confirm the DOI?

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@kbarnhart kbarnhart commented Nov 24, 2019

/ooo November 24 until November 28

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@ooo ooo bot commented Nov 24, 2019

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@paudetseis paudetseis commented Nov 24, 2019

@kbarnhart I am confused about the DOI that you cite (https://doi.org/10.5281/zenodo.203551250), as I have not mentioned that DOI previously nor can I find any reference to it on this page, in the repo, README or API. The one mentioned above is the correct one (https://doi.org/10.5281/zenodo.3551250). The Zenodo badge in the README (https://zenodo.org/badge/latestdoi/204565459) points to the latest DOI for Telewavesim.

Perhaps I misunderstood your final check box about the zenodo DOI: "Please list the Zenodo DOI of the archived version here." Can you please clarify where you found reference to the unresolved DOI for Telewavesim and how I can fix this?

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@ooo ooo bot commented Nov 24, 2019

👋 Hey @paudetseis...

Letting you know, @kbarnhart is currently OOO until Thursday, November 28th 2019. ❤️

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@kbarnhart kbarnhart commented Nov 24, 2019

@paudetseis My apologies. I had meant to type https://doi.org/10.5281/zenodo.3551250
instead of https://doi.org/10.5281/zenodo.203551250. I mistyped and added a "20".

However, I do not find the DO https://doi.org/10.5281/zenodo.3551250 as resolved.

When I try to go to it I get the following screen.

Screen Shot 2019-11-24 at 9 02 21 PM

I then went to the Telewavesim repository and the badge there lists:
10.5281/zenodo.3551258

Screen Shot 2019-11-24 at 8 58 00 PM

So I wanted to verify the correct DOI. I suspect it should be 10.5281/zenodo.3551258

(FYI - I'll be away from internet for 4 days starting mid-day Monday Nov 25th in GMT+12)

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@paudetseis paudetseis commented Nov 25, 2019

@kbarnhart My apologies too - the DOI that I typed here previously (https://doi.org/10.5281/zenodo.3551250) had a typo in the last digit. It should be https://doi.org/10.5281/zenodo.3551258. Sorry for the confusion.

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@ooo ooo bot commented Nov 25, 2019

👋 Hey @paudetseis...

Letting you know, @kbarnhart is currently OOO until Thursday, November 28th 2019. ❤️

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@kbarnhart kbarnhart commented Nov 28, 2019

@whedon set 10.5281/zenodo.3551258 as archive

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@whedon whedon commented Nov 28, 2019

OK. 10.5281/zenodo.3551258 is the archive.

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@kbarnhart kbarnhart commented Nov 28, 2019

@openjournals/joss-eics this is ready for final processing.

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 1, 2019

@paudetseis can you please work on the following:

  • Can you amend the meta data for the archive on Zenodo such that the title and authors match the JOSS paper?
  • The paper contains two instances of allows the, I suggest using allows for the instead.
  • The acronym OBS is defined in the text but never used. Perhaps you can omit the use of the acronym altogether.
  • In the following: ...from core-refracted teleseismic shear waves (i.e., SKS, SKKS), etc., please consider removing , etc., at the end of the sentence. Since the sentence contains such as, it is already clear that what follows is a subset of non-exhaustive examples.
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@paudetseis paudetseis commented Dec 2, 2019

@Kevin-Mattheus-Moerman Thank you for the suggestions.

  • I edited the title and authors on Zenodo to match the JOSS paper.
  • The two instances of allows are not followed by the but rather by a noun and a gerund, respectively, which I believe is correct grammar.
  • I removed the acronym OBS.
  • I amended the sentence and removed , etc. at the end of the sentence.
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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 2, 2019

@whedon generate pdf

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@whedon whedon commented Dec 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 2, 2019

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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 2, 2019

@whedon accept

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@whedon whedon commented Dec 2, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 2, 2019


OK DOIs

- 10.1093/gji/ggw111 is OK
- 10.1785/0120110162 is OK
- 10.1002/2017TC004625 is OK
- 10.1111/j.1365-246X.1984.tb05056.x is OK
- 10.1046/j.1365-246x.2000.00090.x is OK
- 10.1088/1749-4699/8/1/014003 is OK
- 10.1130/L126.1 is OK
- 10.1016/S0031-9201(97)00033-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 2, 2019

Check final proof 👉 openjournals/joss-papers#1138

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1138, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman commented Dec 2, 2019

@whedon accept deposit=true

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@whedon whedon commented Dec 2, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Dec 2, 2019
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@whedon whedon commented Dec 2, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Dec 2, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1139
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01818
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@whedon whedon commented Dec 2, 2019

🎉🎉🎉 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.01818/status.svg)](https://doi.org/10.21105/joss.01818)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01818">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01818/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01818/status.svg
   :target: https://doi.org/10.21105/joss.01818

This is how it will look in your documentation:

DOI

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