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[REVIEW]: Fruitbat: A Python Package for Estimating Redshifts of Fast Radio Bursts #1399

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whedon opened this issue Apr 22, 2019 · 40 comments

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commented Apr 22, 2019

Submitting author: @abatten (Adam Batten)
Repository: https://github.com/abatten/fruitbat
Version: v1.0.1
Editor: @xuanxu
Reviewer: @zingale
Archive: 10.5281/zenodo.2667596

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/634bb69f2445c7457bea5dbc0b83e650"><img src="http://joss.theoj.org/papers/634bb69f2445c7457bea5dbc0b83e650/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/634bb69f2445c7457bea5dbc0b83e650/status.svg)](http://joss.theoj.org/papers/634bb69f2445c7457bea5dbc0b83e650)

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

@zingale, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @xuanxu know.

Please try and complete your review in the next two weeks

Review checklist for @zingale

Conflict of interest

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?
  • Version: v1.0.1
  • Authorship: Has the submitting author (@abatten) 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 function 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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commented Apr 22, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @zingale it looks like you're currently assigned as the reviewer for 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:

watching

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

notifications

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

@whedon commands
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commented Apr 22, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Apr 22, 2019

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commented Apr 28, 2019

added an issue about installing: abatten/fruitbat#27

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commented Apr 28, 2019

adding an issue about reproducing the simple example: abatten/fruitbat#29

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commented May 1, 2019

There are two more issues to be resolved:

abatten/fruitbat#32
abatten/fruitbat#31

otherwise, it looks good.

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commented May 2, 2019

I have fixed all the issues that you mentioned it the last couple of pull requests.

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commented May 2, 2019

Whilst we are here, do you know if it is possible to get the TeX files that produce the JOSS paper? This would be required if I want to submit the paper to the ArXiv. I just tested it with the PDF created by Whedon and it was rejected, requesting for all the TeX files instead of a PDF.

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commented May 2, 2019

@xuanxu all of my issues have been address and I've completed the checklist and accept this for publication.

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commented May 2, 2019

@abatten regarding the TeX files, unfortunately the conversion using Pandoc happens automatically with our whedon bot, so it isn't super easy to get those files. You may be able to do the conversion yourself manually based on the LaTeX template here: https://github.com/openjournals/whedon/tree/master/resources

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commented May 2, 2019

Thanks @zingale!

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commented May 2, 2019

@whedon generate pdf

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commented May 2, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 2, 2019

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commented May 2, 2019

@whedon check references

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commented May 2, 2019

Attempting to check references...
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commented May 2, 2019


OK DOIs

- 10.1126/science.1147532 is OK
- 10.1126/science.1236789 is OK
- 10.1093/mnras/stv1953 is OK
- 10.1038/s41586-018-0867-7 is OK
- 10.1017/pasa.2016.35 is OK
- 10.3847/1538-4357/aa7d57 is OK
- 10.3847/2041-8213/834/2/L7 is OK
- 10.1086/380598 is OK
- 10.1111/j.1365-2966.2004.07359.x is OK
- 10.3847/2041-8213/aae8e3 is OK
- 10.1088/0067-0049/180/2/330 is OK
- 10.1088/0067-0049/192/2/18 is OK
- 10.1088/0067-0049/208/2/19 is OK
- 10.1051/0004-6361/201321591 is OK
- 10.1051/0004-6361/201525830 is OK
- 10.3847/1538-4357/835/1/29 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented May 2, 2019

@abatten Could you please release a new version with all the recent changes?
Once you do that I need you to create an archive of that version in zenodo/figshare/other and report the DOI here.

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commented May 5, 2019

I made a new release: 1.0.1 so this will have to be updated in the paper.
Archive version: 10.5281/zenodo.2667568

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commented May 5, 2019

@abatten I can't find the new release listed in GitHub: https://github.com/abatten/fruitbat/releases

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commented May 5, 2019

Ah I fixed that. There should be the new release 1.0.1.

Also, I messed up the files in the Zenodo archive so I had to make a new zenodo doi: 10.5281/zenodo.2667596

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commented May 5, 2019

Great, thanks @abatten!

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commented May 5, 2019

@whedon set v1.0.1 as version

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commented May 5, 2019

OK. v1.0.1 is the version.

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commented May 5, 2019

@whedon generate pdf

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commented May 5, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented May 5, 2019

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commented May 5, 2019

@whedon set 10.5281/zenodo.2667596 as archive

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commented May 5, 2019

OK. 10.5281/zenodo.2667596 is the archive.

@xuanxu xuanxu added the accepted label May 5, 2019

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commented May 5, 2019

This is ready now for publication.
Pinging EIC for final acceptance: @openjournals/joss-eics

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commented May 5, 2019

Thanks @xuanxu. CrossRef is having some issues right now, so we are going to pause on publishing accepted articles until those issues are resolved.

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commented May 9, 2019

@whedon accept

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commented May 9, 2019

Attempting dry run of processing paper acceptance...
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commented May 9, 2019


OK DOIs

- 10.1126/science.1147532 is OK
- 10.1126/science.1236789 is OK
- 10.1093/mnras/stv1953 is OK
- 10.1038/s41586-018-0867-7 is OK
- 10.1017/pasa.2016.35 is OK
- 10.3847/1538-4357/aa7d57 is OK
- 10.3847/2041-8213/834/2/L7 is OK
- 10.1086/380598 is OK
- 10.1111/j.1365-2966.2004.07359.x is OK
- 10.3847/2041-8213/aae8e3 is OK
- 10.1088/0067-0049/180/2/330 is OK
- 10.1088/0067-0049/192/2/18 is OK
- 10.1088/0067-0049/208/2/19 is OK
- 10.1051/0004-6361/201321591 is OK
- 10.1051/0004-6361/201525830 is OK
- 10.3847/1538-4357/835/1/29 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented May 9, 2019

Check final proof 👉 openjournals/joss-papers#671

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#671, 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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commented May 9, 2019

@whedon accept deposit=true

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commented May 9, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented May 9, 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#672
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01399
  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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commented May 9, 2019

Congratulations, @abatten, your JOSS paper is now published! 🎉

With huge thanks to our editor: @xuanxu, and the reviewer: @zingale — we couldn't do this without you! 🙏

@labarba labarba closed this May 9, 2019

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commented May 9, 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](http://joss.theoj.org/papers/10.21105/joss.01399/status.svg)](https://doi.org/10.21105/joss.01399)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01399">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01399/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01399/status.svg
   :target: https://doi.org/10.21105/joss.01399

This is how it will look in your documentation:

DOI

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