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[REVIEW]: CluSim: a Python package for the comparison of clusterings and dendrograms #1264

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @ajgates42 (Alexander Gates) Repository: https://github.com/Hoosier-Clusters/clusim Version: v0.3.2 Editor: @VivianePons Reviewers: @pajaskowiak, @adavidzh Archive: 10.5281/zenodo.2601868

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c"><img src="http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c/status.svg)](http://joss.theoj.org/papers/16ce8a38d204c773202405e1c7da518c)

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

@pajaskowiak, 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 @VivianePons know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @pajaskowiak

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @adavidzh

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ajgates42 commented 5 years ago

Thats the standard citation from the scipy website https://www.scipy.org/citing.html. But the reference isn't essential for the work, so lets, just drop it from the paper. I've updated the bib accordingly.

Thanks!

On Wed, Mar 20, 2019 at 6:10 AM Arfon Smith notifications@github.com wrote:

Also the date on the scipy citation prints weirdly, @arfon https://github.com/arfon do you know if it's the correct way to do it?

Not sure, I think it's probably because of the bibtex entry not actually having a date range https://github.com/Hoosier-Clusters/clusim/blob/master/paper.bib#L85

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-474766604, or mute the thread https://github.com/notifications/unsubscribe-auth/AZk97YxfMP0P4ptn0Pr-ffoqjdaz_SScks5vYgkpgaJpZM4bDUad .

-- Alexander Gates Postdoctoral Research Scholar Center for Complex Network Research Northeastern University http://alexandergates.net

VivianePons commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

VivianePons commented 5 years ago

@whedon check references

whedon commented 5 years ago 
Attempting to check references...
whedon commented 5 years ago 

OK DOIs

- 10.1007/BF01908075 is OK
- 10.1145/331499.331504 is OK
- 10.1186/1471-2105-9-497 is OK
- 10.1145/1553374.1553511 is OK
- 10.1101/196840 is OK
- 10.1093/bioinformatics/btq228 is OK

MISSING DOIs

- None

INVALID DOIs

- None
VivianePons commented 5 years ago

Perfect, could you update the Zenodo metadata so that the title matches the paper name? (At the moment, the Zenodo title is only "CluSim" whereas the title paper is: "CluSim: a Python package for the comparison of clusterings and dendrograms")

Also, you might wanna udpate the paper.md and paper.bib on the the Zenodo archive if that's possible (sorry, I should probably have asked you to create the archive AFTER checking the references)

ajgates42 commented 5 years ago

OK. The Zenodo metadata and files have been brought up to date. The new DOI is 10.5281/zenodo.2601868

On Wed, Mar 20, 2019 at 5:50 PM Viviane Pons notifications@github.com wrote:

Perfect, could you update the Zenodo metadata so that the title matches the paper name? (At the moment, the Zenodo title is only "CluSim" whereas the title paper is: "CluSim: a Python package for the comparison of clusterings and dendrograms")

Also, you might wanna udpate the paper.md and paper.bib on the the Zenodo archive if that's possible (sorry, I should probably have asked you to create the archive AFTER checking the references)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-475042484, or mute the thread https://github.com/notifications/unsubscribe-auth/AZk97dNC-iBOWgBWa9c9VPXLi05V_06-ks5vYq0-gaJpZM4bDUad .

-- Alexander Gates Postdoctoral Research Scholar Center for Complex Network Research Northeastern University http://alexandergates.net

VivianePons commented 5 years ago

@whedon set 10.5281/zenodo.2601868 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.2601868 is the archive.

VivianePons commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

VivianePons commented 5 years ago

Thank you @ajgates42 @adavidzh and @pajaskowiak for the great work! This paper is ready to be accepted. It's now up to you @openjournals/joss-eics

arfon commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/572

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/572, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
whedon commented 5 years ago 

OK DOIs

- 10.1007/BF01908075 is OK
- 10.1145/331499.331504 is OK
- 10.1186/1471-2105-9-497 is OK
- 10.1145/1553374.1553511 is OK
- 10.1101/196840 is OK
- 10.1093/bioinformatics/btq228 is OK

MISSING DOIs

- None

INVALID DOIs

- None
arfon commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 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/573
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01264
  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...

arfon commented 5 years ago

@pajaskowiak, @adavidzh - many thanks for your reviews here and to @VivianePons for editing this submission :sparkles:

@ajgates42 - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 5 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](http://joss.theoj.org/papers/10.21105/joss.01264/status.svg)](https://doi.org/10.21105/joss.01264)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01264">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01264/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01264/status.svg
   :target: https://doi.org/10.21105/joss.01264

This is how it will look in your documentation:

DOI

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ajgates42 commented 5 years ago

Awesome! Thank you everyone for the insightful feedback and great submission experience.

On Thu, Mar 21, 2019 at 1:21 PM Arfon Smith notifications@github.com wrote:

@pajaskowiak https://github.com/pajaskowiak, @adavidzh https://github.com/adavidzh - many thanks for your reviews here and to @VivianePons https://github.com/VivianePons for editing this submission ✨

@ajgates42 https://github.com/ajgates42 - your paper is now accepted into JOSS ⚡️🚀💥

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1264#issuecomment-475324779, or mute the thread https://github.com/notifications/unsubscribe-auth/AZk97b3SyOZSOPb8mchVmo5WDnZa-1bIks5vY7-CgaJpZM4bDUad .

-- Alexander Gates Postdoctoral Research Scholar Center for Complex Network Research Northeastern University http://alexandergates.net