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[REVIEW]: Your: Your Unified Reader #2750

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @KshitijAggarwal (Kshitij Aggarwal) Repository: https://github.com/thepetabyteproject/your Version: 0.6.0 Editor: @dfm Reviewer: @pravirkr, @paulray Archive: 10.5281/zenodo.4269947

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Status

status

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HTML: <a href="https://joss.theoj.org/papers/798844ebd352f563de28bb75515da674"><img src="https://joss.theoj.org/papers/798844ebd352f563de28bb75515da674/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/798844ebd352f563de28bb75515da674/status.svg)](https://joss.theoj.org/papers/798844ebd352f563de28bb75515da674)

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

@pravirkr & @paulray, 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 @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 @pravirkr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @paulray

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/mnras/staa1927 is OK
- 10.1111/j.1745-3933.2010.00882.x is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1109/mcse.2011.37 is OK
- 10.1071/AS04022 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2012.20622.x is OK
- 10.1093/mnras/staa1856 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:

pravirkr commented 3 years ago

The software package your is well-organized with a nice interface. The documentation is very detailed with lots of good examples. This package is going to be very useful for the FRB/radio transients science.

I have opened the following issues within the main repository:

Most of these are very minor issues. Apologies for nitpicking (reviewing for the first time).

KshitijAggarwal commented 3 years ago

@pravirkr, thanks for the issues. We have addressed those from our end, feel free to take a look and close them.

paulray commented 3 years ago

I'm supposed to answer this question: "Does the full list of paper authors seem appropriate and complete?" I don't know how to judge that, other than from git commits. Is there a statement of the various author contributions somewhere? I didn't see it in the paper.

KshitijAggarwal commented 3 years ago

Hi @paulray, I can answer that here: @KshitijAggarwal @devanshkv: equal contribution in terms of code, ideas, discussion, structure and documentation @scottransom: original author of psrfits, which was modified for your @demorest: original author of pysigproc, which was modified for your @ReshmaAnnaThomas and @wcfiore: wrote + contributed to filwriter.py @josephwkania: worked on RFI mitigation functions, your_viewer @xiggystardust, Duncan Lorimer, Maura McLaughlin, @nategarver-daniels: contributed through discussions and structure @rwharton: original author of fitswriter, which was then modified for your

paulray commented 3 years ago

Thanks, that is extremely helpful!

paulray commented 3 years ago

Regarding my review, I want to disclose the following potential COIs.

I just now realized that the submitting author is a NANOGrav member. I don't think that is a serious conflict since I wasn't even aware of it. According to the statement above, my other potential COIs generally have a largely advisory role in this project or have prior code that was subsumed into this project.

I don't think these potential COIs affect my ability to make an impartial review, so I propose that they be waived.

dfm commented 3 years ago

@paulray: Thanks for bringing these up! I agree that these potential conflicts seem ok to be waived.

@KshitijAggarwal: do you or co-authors don't have any concerns about this? Please feel free to let me know here or offline via email if you'd prefer. Thanks!

KshitijAggarwal commented 3 years ago

@dfm @paulray: We don't have any concerns regarding this.

paulray commented 3 years ago

I enjoyed reviewing the paper and the code and trying it out on same data I had. I found it well explained, easy to install and the documentation was very clear. Nice work!

KshitijAggarwal commented 3 years ago

@pravirkr @dfm, we are submitting an NSF proposal for a project (the petabyte project) which is going to rely on this library. The NSF proposal is due pretty soon. I also noticed that only a few checklist items are left in the review. So I wanted to ask if it would be possible to complete this review in the next day or so? This way we can properly cite it in our proposal, and also upload it to arxiv. If not, is it okay if we upload the paper to arxiv before the review process is complete?

dfm commented 3 years ago

You're welcome to post the pre-print to ArXiv, but sometimes ArXiv doesn't accept JOSS papers so no guarantees that it will work!

@pravirkr: you definitely shouldn't feel pressured to finish your review faster than planned!

pravirkr commented 3 years ago

@dfm: Thanks. I was waiting for the resolution of the above issues. @KshitijAggarwal: Thanks for addressing the issues. Looks good now! The only thing left to do IMO is to release the updated version (0.5.9, I guess).

I also recommend acceptance of this work.

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

- 10.1093/mnras/staa1927 is OK
- 10.1111/j.1745-3933.2010.00882.x is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1109/mcse.2011.37 is OK
- 10.1071/AS04022 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2012.20622.x is OK
- 10.1093/mnras/staa1856 is OK

MISSING DOIs

- None

INVALID DOIs

- None
dfm commented 3 years ago

@pravirkr, @paulray: Thanks for your reviews!!

@KshitijAggarwal: I'm going to go through the paper and do some final checks. Then I'll give you a few instructions to prepare for final review. This will include minting a new release so no need to do that yet!

KshitijAggarwal commented 3 years ago

@pravirkr, @paulray: thanks for the reviews and useful comments!

@dfm: Thanks and that sounds good!

dfm commented 3 years ago

@KshitijAggarwal: I've just submitted a small pull request with some formatting changes. After you take a look at that, here are the steps to run:

  1. Comment @whedon generate pdf on this thread and carefully read through the manuscript to make sure that you're happy with it because it can be hard to update later. You should especially double check author names and affiliations.
  2. Update the version number on the software and create an archive of that release (using Zenodo or similar) and report the archive DOI and new version number to this thread. NOTE: The title and author list in the archive metadata must exactly match this manuscript (you can generally update the metadata even after the archive has been made).

Let me know if you have any issues or questions!

KshitijAggarwal 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:

KshitijAggarwal commented 3 years ago

@dfm, I have looked at the manuscript and no changes are required. All the details are correct.

Here is the DOI of the archive: 10.5281/zenodo.4269947, and the new version number is 0.6.0

DOI

I have edited the title and author list in the archive to be exactly the same as that in this manuscript.

dfm commented 3 years ago

@whedon set 10.5281/zenodo.4269947 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4269947 is the archive.

dfm commented 3 years ago

@whedon set 0.6.0 as version

whedon commented 3 years ago

OK. 0.6.0 is the version.

dfm commented 3 years ago

@KshitijAggarwal: I found a few more remaining formatting issues with the manuscript. Take a look at that PR and then we should be good to go!

devanshkv commented 3 years ago

@dfm merged!

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

- 10.1093/mnras/staa1927 is OK
- 10.1111/j.1745-3933.2010.00882.x is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1071/AS04022 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2012.20622.x is OK
- 10.1093/mnras/staa1856 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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

- 10.1093/mnras/staa1927 is OK
- 10.1111/j.1745-3933.2010.00882.x is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1071/AS04022 is OK
- 10.1145/2833157.2833162 is OK
- 10.1111/j.1365-2966.2012.20622.x is OK
- 10.1093/mnras/staa1856 is OK
- 10.1038/s41586-020-2649-2 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/1907

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1907, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
dfm commented 3 years ago

An editor-in-chief will take a final look at this submission and then we should be good to go.

Thanks again @pravirkr and @paulray for your reviews!!

devanshkv commented 3 years ago

Thanks, @dfm, @pravirkr, and @paulray.

KshitijAggarwal commented 3 years ago

Thanks a lot, @dfm, @pravirkr, and @paulray!!

josephwkania commented 3 years ago

Thanks @dfm, @pravirkr, @paulray! 😊

kthyng 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:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1912
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02750
  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...

kthyng commented 3 years ago

Congrats on your new publication @KshitijAggarwal! Many thanks to editor @dfm and reviewers @pravirkr and @paulray for your time and expertise!! 🎉

whedon commented 3 years ago

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

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.02750/status.svg)](https://doi.org/10.21105/joss.02750)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02750">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02750/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02750/status.svg
   :target: https://doi.org/10.21105/joss.02750

This is how it will look in your documentation:

DOI

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KshitijAggarwal commented 3 years ago

Thanks a lot, everyone!!! :) :)