[REVIEW]: Riroriro: Simulating gravitational waves and calculating SNRs in Python

whedon commented 3 years ago

Submitting author: @wvanzeist (Wouter van Zeist) Repository: https://github.com/wvanzeist/riroriro Version: v1.0.0 Editor: @dfm Reviewer: @GregoryAshton, @katiebreivik Archive: 10.5281/zenodo.4588070

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Status

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Markdown: [![status](https://joss.theoj.org/papers/22ee68e9828487b9d7b0036b195b99ad/status.svg)](https://joss.theoj.org/papers/22ee68e9828487b9d7b0036b195b99ad)

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

@GregoryAshton & @katiebreivik, 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 @dfm 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 @GregoryAshton

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wvanzeist) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @katiebreivik

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wvanzeist) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

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

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

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whedon commented 3 years ago

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

OK DOIs

- 10.1088/1361-6404/aaf81e is OK
- 10.1103/PhysRevD.95.024038 is OK
- 10.1093/mnras/sty908 is OK
- 10.1103/PhysRevD.85.122006 is OK
- 10.1103/PhysRevD.52.605 is OK
- 10.1103/PhysRevD.67.024016 is OK
- 10.1088/0264-9381/24/19/S31 is OK
- 10.1103/PhysRevD.59.084006 is OK
- 10.1103/PhysRevD.65.044001 is OK
- 10.1103/PhysRevD.65.124012 is OK
- 10.1103/PhysRevX.4.031006 is OK
- 10.1017/pasa.2017.51 is OK
- 10.1093/mnras/sty1353 is OK
- 10.21105/joss.01987 is OK
- 10.1103/PhysRevLett.116.061102 is OK
- 10.3847/1538-4365/ab06fc is OK
- 10.1088/1538-3873/aaef0b is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

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

GregoryAshton commented 3 years ago

@dfm I'm unable to tick the boxes above (I am logged in, and I accepted the request a few days back - now the link gives a "Sorry, we couldn't find that repository invitation")

dfm commented 3 years ago

@GregoryAshton: Sorry about that - I'll send you a new invitation!

dfm commented 3 years ago

@whedon re-invite @GregoryAshton as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

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

whedon commented 3 years ago

:wave: @GregoryAshton, please update us on how your review is going.

whedon commented 3 years ago

:wave: @katiebreivik, please update us on how your review is going.

dfm commented 3 years ago

@GregoryAshton, @katiebreivik: Note that the messages from @whedon are automated, and I am following along with issues that you have already opened. No need for more details here. Let me know if you have any questions as the reviews proceed!

wvanzeist commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

wvanzeist commented 3 years ago

I have responded to every issue that has been raised in the repository; is there anything else that is keeping the review from proceeding?

katiebreivik commented 3 years ago

Hi @wvanzeist -- apologies on my part!! I am reading through the new proof this evening since I've been swamped for the past week.

katiebreivik commented 3 years ago

I am happy to recommend for publishing -- all boxes checked!

wvanzeist commented 3 years ago

@GregoryAshton Have you seen my response to the issue you raised in the Riroriro directory?

GregoryAshton commented 3 years ago

All boxes checked. Happy to recommend for publication.

dfm commented 3 years ago

Awesome - thanks @GregoryAshton and @katiebreivik for your reviews!

@wvanzeist: Now that the reviewers have signed off I'm going to do a pass of editing and then I'll have a few more steps for you in the next couple of days.

dfm commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

dfm commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1088/1361-6404/aaf81e is OK
- 10.1103/PhysRevD.95.024038 is OK
- 10.1093/mnras/sty908 is OK
- 10.1103/PhysRevD.85.122006 is OK
- 10.1017/pasa.2017.51 is OK
- 10.1093/mnras/sty1353 is OK
- 10.21105/joss.01987 is OK
- 10.1103/PhysRevLett.116.061102 is OK
- 10.7935/GT1W-FZ16 is OK
- 10.1103/PhysRevD.102.044055 is OK

MISSING DOIs

- None

INVALID DOIs

- None

dfm commented 3 years ago

@wvanzeist: I've opened a tiny pull request with some minor edits to the paper. Can you take a look at that and once you've merged, please take the following steps:

Comment @whedon generate pdf on this thread and read through the manuscript to make sure that you're happy with it (it's hard to make changes later!), especially author names and affiliations.
Increment the version number of the software and report that version number back here.
Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

Let me know if you have questions or run into any issues!

wvanzeist commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

wvanzeist commented 3 years ago

@dfm Would you know of a way to prevent the PDF from breaking the word "Riroriro" weirdly without a line-break hyphen at line 62?

In the meantime, I have set the version number to 1.0.0 and created a Zenodo archive, which is at the following DOI: 10.5281/zenodo.4588070

Also, because of your suggestion to tweak the title slightly I had a discussion about it with my co-authors and adjusted it a bit more to be more representative and elegant, replacing "calculating signal-to-noise ratios" with "evaluating their detectability".

wvanzeist commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

wvanzeist commented 3 years ago

In order to deal with the weird line break at line 62, I decided to just rearrange the sentence so that the word with the special formatting wasn't at the end of the line. It's fixed now.

wvanzeist commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

dfm commented 3 years ago

Sounds good - sorry that I didn't have a suggestion sooner!

wvanzeist commented 3 years ago

@wvanzeist: I've opened a tiny pull request with some minor edits to the paper. Can you take a look at that and once you've merged, please take the following steps:

Comment @whedon generate pdf on this thread and read through the manuscript to make sure that you're happy with it (it's hard to make changes later!), especially author names and affiliations.

Increment the version number of the software and report that version number back here.

Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

Let me know if you have questions or run into any issues!

I have completed each of these steps, is there anything else I need to do now?

dfm commented 3 years ago

@wvanzeist: whoops! I hadn't seen the DOI and version number in the previous comment - sorry! I think you're all set. I'll pass this off to the Editors in Chief who might have some final edits before final processing.

@GregoryAshton, @katiebreivik: thanks again for your reviews!!

dfm commented 3 years ago

@whedon set 10.5281/zenodo.4588070 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4588070 is the archive.

dfm commented 3 years ago

@whedon set v1.0.0 as version

whedon commented 3 years ago

OK. v1.0.0 is the version.

dfm commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1088/1361-6404/aaf81e is OK
- 10.1103/PhysRevD.95.024038 is OK
- 10.1093/mnras/sty908 is OK
- 10.1103/PhysRevD.85.122006 is OK
- 10.1017/pasa.2017.51 is OK
- 10.1093/mnras/sty1353 is OK
- 10.21105/joss.01987 is OK
- 10.1103/PhysRevLett.116.061102 is OK
- 10.7935/GT1W-FZ16 is OK
- 10.1103/PhysRevD.102.044055 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2139

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2139, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/2140
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02968
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 3 years ago

Congratulations @wvanzeist on your article's publication in JOSS!

Many thanks to @GregoryAshton and @katiebreivik for reviewing this, and @dfm for editing it.

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02968">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02968/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02968/status.svg
   :target: https://doi.org/10.21105/joss.02968

This is how it will look in your documentation:

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wvanzeist commented 3 years ago

Great thanks for all the reviewers and editors!

@kyleniemeyer When I go to the theoj.org page for this article, the place where the PDF is supposed to be appears empty, and clicking "download paper" gives "file not found". Might there be a bug of some sort, or is it just taking some time for the website to update?

kyleniemeyer commented 3 years ago

@wvanzeist yeah, sometimes I have found that caches / different DNS resolvers (or something) take a bit for the PDF to propagate and become available. It loads fine for me, so I would just give it some time on your end.

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