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[REVIEW]: ExTemp: A computational and image-processing suite for extracting temporal barcodes #2026

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whedon opened this issue Jan 17, 2020 · 41 comments
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@whedon whedon commented Jan 17, 2020

Submitting author: @shalinshah1993 (Shalin Shah)
Repository: https://github.com/shalinshah1993/temporalDNAbarcodes
Version: 1.0.0
Editor: @csoneson
Reviewer: @lbugnon, @SirSharpest, @RealPolitiX
Archive: 10.5281/zenodo.3660411

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/73c6bcf3245062f7e20242c3cb68fe82"><img src="https://joss.theoj.org/papers/73c6bcf3245062f7e20242c3cb68fe82/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/73c6bcf3245062f7e20242c3cb68fe82/status.svg)](https://joss.theoj.org/papers/73c6bcf3245062f7e20242c3cb68fe82)

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

@lbugnon & @SirSharpest & @RealPolitiX, 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 @csoneson know.

Please try and complete your review in the next two weeks

Review checklist for @lbugnon

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 (@shalinshah1993) 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 @SirSharpest

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 (@shalinshah1993) 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 @RealPolitiX

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 (@shalinshah1993) 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 Jan 17, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lbugnon, @SirSharpest, @RealPolitiX 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:

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

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 Jan 17, 2020

Reference check summary:

OK DOIs

- 10.1021/acssynbio.9b00010 is OK
- 10.1007/978-3-030-00030-1_5 is OK
- 10.1021/acs.nanolett.9b00590 is OK
- 10.1364/OE.22.015982 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Jan 17, 2020

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@csoneson csoneson commented Jan 17, 2020

@lbugnon, @SirSharpest, @RealPolitiX - this is where the review happens! Please check the reviewer instructions in the issue above, and don't hesitate to ping me if you have questions.

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@csoneson csoneson commented Jan 31, 2020

👋 @lbugnon, @SirSharpest, @RealPolitiX - I just wanted to check in on your reviews. Do you have an update on when you think you would be able to provide some comments for @shalinshah1993 (I see that @SirSharpest has opened an issue in the repo)?

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@SirSharpest SirSharpest commented Jan 31, 2020

👋 @lbugnon, @SirSharpest, @RealPolitiX - I just wanted to check in on your reviews. Do you have an update on when you think you would be able to provide some comments for @shalinshah1993 (I see that @SirSharpest has opened an issue in the repo)?

Yes, I'll have my review finished before Monday, I think that all my issues are addressed and just need to verify before I can sign off.

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@lbugnon lbugnon commented Feb 3, 2020

All my issues have been addressed, I think it is a good work and ready to publish

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@SirSharpest SirSharpest commented Feb 3, 2020

I'm happy to sign off on also.

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@csoneson csoneson commented Feb 4, 2020

Thanks @lbugnon , @SirSharpest for your reviews.

@lbugnon - there are still some unchecked items in your checklist above. Could you confirm that these issues have been addressed, and if so, check the boxes?

@RealPolitiX - could you provide an update on your review status?

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@shalinshah1993 shalinshah1993 commented Feb 7, 2020

Dear @csoneson, just following up if we have any progress here?

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@csoneson csoneson commented Feb 7, 2020

@shalinshah1993 I'd like to hear from @RealPolitiX as well. I have reached out for an update via email.

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@RealPolitiX RealPolitiX commented Feb 7, 2020

Nice work, ready for publication

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@csoneson csoneson commented Feb 9, 2020

@whedon generate pdf

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@whedon whedon commented Feb 9, 2020

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@csoneson csoneson commented Feb 9, 2020

@whedon check references

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@whedon whedon commented Feb 9, 2020

Reference check summary:

OK DOIs

- 10.1021/acssynbio.9b00010 is OK
- 10.1007/978-3-030-00030-1_5 is OK
- 10.1021/acs.nanolett.9b00590 is OK
- 10.1364/OE.22.015982 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@csoneson csoneson commented Feb 9, 2020

👋 @shalinshah1993 - I have gone through your manuscript and sent a few suggestions in a PR. Could you please check, merge and generate a new proof here with @whedon generate pdf?

Next, please:

  • check that the version information is consistently reported and report the version back here
  • create a tagged release
  • generate a zenodo archive
  • make sure that the title and authors of the zenodo archive are identical to those of the paper (you can also add the ORCID of the authors there)
  • report back here with the DOI of the zenodo archive

Finally, I would suggest to add also the JOSS paper to your README, and make it clear to users which of the papers to cite in which situation.

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@shalinshah1993 shalinshah1993 commented Feb 9, 2020

Dear @csoneson you said you sent a few suggestions in PR. I'm sorry where did you send it?

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@csoneson csoneson commented Feb 9, 2020

Oops, sorry, forgot to press send...should be there now.

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@csoneson csoneson commented Feb 9, 2020

For the Zenodo archive, please make sure that the title and author list are identical to those of the paper

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@shalinshah1993 shalinshah1993 commented Feb 9, 2020

Oh great, I accepted your PR. Thank you for those edits.

I think the authors' names and paper names should match now.
https://zenodo.org/record/3660411#.XkARhxNKjVo

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@csoneson csoneson commented Feb 9, 2020

@whedon generate pdf

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@whedon whedon commented Feb 9, 2020

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@csoneson csoneson commented Feb 9, 2020

@whedon set 10.5281/zenodo.3660411 as archive

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@whedon whedon commented Feb 9, 2020

OK. 10.5281/zenodo.3660411 is the archive.

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@csoneson csoneson commented Feb 9, 2020

@whedon set 1.0.0 as version

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@whedon whedon commented Feb 9, 2020

OK. 1.0.0 is the version.

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@csoneson csoneson commented Feb 9, 2020

@whedon accept

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@whedon whedon commented Feb 9, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 9, 2020

Reference check summary:

OK DOIs

- 10.1021/acssynbio.9b00010 is OK
- 10.1007/978-3-030-00030-1_5 is OK
- 10.1021/acs.nanolett.9b00590 is OK
- 10.1364/OE.22.015982 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Feb 9, 2020

Check final proof 👉 openjournals/joss-papers#1285

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1285, 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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@csoneson csoneson commented Feb 9, 2020

@openjournals/joss-eics - I believe this paper is ready to be accepted!

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@csoneson csoneson commented Feb 9, 2020

@shalinshah1993 - I think this all looks good. I've handed it over to the EiCs for the final check and acceptance.

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@shalinshah1993 shalinshah1993 commented Feb 9, 2020

Thank you very much @csoneson for all your help and edits. Also, thank you @SirSharpest @lbugnon @RealPolitiX for your comments and feedback.

I think overall the Extemp package and GitHub repo look a lot more professional and clean. I'm happy that I submitted it to JOSS for peer-review.

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@kthyng kthyng commented Feb 9, 2020

Everything looks great! You all made my job very easy!

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@kthyng kthyng commented Feb 9, 2020

@whedon accept deposit=true

@whedon whedon added the accepted label Feb 9, 2020
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@whedon whedon commented Feb 9, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Feb 9, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Feb 9, 2020

🚨🚨🚨 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#1286
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02026
  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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@kthyng kthyng commented Feb 9, 2020

Congratulations to @shalinshah1993 on your new publication! Thanks to @csoneson for editing and to @lbugnon, @SirSharpest, and @RealPolitiX for reviewing — we relied on your time and expertise!

@kthyng kthyng closed this Feb 9, 2020
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@whedon whedon commented Feb 9, 2020

🎉🎉🎉 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.02026/status.svg)](https://doi.org/10.21105/joss.02026)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02026">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02026/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02026/status.svg
   :target: https://doi.org/10.21105/joss.02026

This is how it will look in your documentation:

DOI

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