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[REVIEW]: Badread: simulation of error-prone long reads #1316

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whedon opened this Issue Mar 12, 2019 · 31 comments

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whedon commented Mar 12, 2019

Submitting author: @rrwick (Ryan Wick)
Repository: https://github.com/rrwick/Badread
Version: v0.1.3
Editor: @brainstorm
Reviewer: @betteridiot
Archive: 10.5281/zenodo.2622997

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/a9ae38312391668801949ddc59e10cb1"><img src="http://joss.theoj.org/papers/a9ae38312391668801949ddc59e10cb1/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/a9ae38312391668801949ddc59e10cb1/status.svg)](http://joss.theoj.org/papers/a9ae38312391668801949ddc59e10cb1)

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) 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

@betteridiot, 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 @brainstorm know.

Please try and complete your review in the next two weeks

Review checklist for @betteridiot

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: Does the release version given match the GitHub release (v0.1.3)?
  • Authorship: Has the submitting author (@rrwick) 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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whedon commented Mar 12, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @betteridiot 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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whedon commented Mar 12, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 12, 2019

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betteridiot commented Mar 22, 2019

Actively working on the review right now. It will be a compilation of steps, and will post the issues once it is done.

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betteridiot commented Mar 25, 2019

Please check rrwick/Badread#2 for my review process notes.

The minor issues raised were:

All in all, terrific work on the package: clean, organized, great test coverage, and excellent documentation.

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betteridiot commented Mar 25, 2019

Once these minor issues are addressed, I would be more than happy to check the remaining boxes and give my support for publication.

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rrwick commented Apr 1, 2019

Thanks for the feedback! I think I've addressed all your points in the relevant issues pages on the Badread wiki.

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betteridiot commented Apr 1, 2019

Thank you @rrwick. @brainstorm this article is good to go on my end.

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brainstorm commented Apr 1, 2019

@whedon check references

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whedon commented Apr 1, 2019

Attempting to check references...
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whedon commented Apr 1, 2019


OK DOIs

- 10.1038/550285a is OK
- 10.1101/gr.223057.117 is OK
- 10.1101/071282 is OK
- 10.1016/j.ygeno.2015.11.003 is OK
- 10.1093/bioinformatics/btr708 is OK
- 10.1093/bioinformatics/bts649 is OK
- 10.1093/bioinformatics/btw602 is OK
- 10.1093/gigascience/gix010 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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brainstorm commented Apr 1, 2019

Great, thanks much @betteridiot. @rrwick, can you please generate a Zenodo DOI for archival purposes?

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rrwick commented Apr 3, 2019

Okay, I've made a Zenodo DOI (https://zenodo.org/record/2622997) and added this shiny new badge to Badread's README:
DOI

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brainstorm commented Apr 4, 2019

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whedon commented Apr 4, 2019

https://zenodo.org/record/2622997 doesn't look like an archive DOI.

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brainstorm commented Apr 4, 2019

@whedon set 10.5281/zenodo.2622997 as archive

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whedon commented Apr 4, 2019

OK. 10.5281/zenodo.2622997 is the archive.

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brainstorm commented Apr 4, 2019

@danielskatz, I think we are done here, ready to accept!

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kyleniemeyer commented Apr 4, 2019

@whedon generate pdf

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whedon commented Apr 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Apr 4, 2019

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kyleniemeyer commented Apr 4, 2019

@whedon accept

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whedon commented Apr 4, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Apr 4, 2019


OK DOIs

- 10.1038/550285a is OK
- 10.1101/gr.223057.117 is OK
- 10.1101/071282 is OK
- 10.1016/j.ygeno.2015.11.003 is OK
- 10.1093/bioinformatics/btr708 is OK
- 10.1093/bioinformatics/bts649 is OK
- 10.1093/bioinformatics/btw602 is OK
- 10.1093/gigascience/gix010 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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whedon commented Apr 4, 2019

Check final proof 👉 openjournals/joss-papers#605

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#605, 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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kyleniemeyer commented Apr 4, 2019

@whedon accept deposit=true

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whedon commented Apr 4, 2019

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

@whedon whedon added the accepted label Apr 4, 2019

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whedon commented Apr 4, 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#606
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01316
  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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kyleniemeyer commented Apr 4, 2019

Congrats @rrwick on your JOSS article acceptance! Thanks to @betteridiot for reviewing and @brainstorm for editing.

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whedon commented Apr 4, 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.01316/status.svg)](https://doi.org/10.21105/joss.01316)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01316">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01316/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01316/status.svg
   :target: https://doi.org/10.21105/joss.01316

This is how it will look in your documentation:

DOI

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:

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rrwick commented Apr 4, 2019

Thanks to everyone involved - much appreciated!

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