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[REVIEW]: Kepler Mapper: A flexible Python implementation of the Mapper algorithm. #1315

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @sauln (Nathaniel Saul) Repository: https://github.com/scikit-tda/kepler-mapper Version: 1.3.3 Editor: @leouieda Reviewer: @ixjlyons, @lmcinnes Archive: 10.5281/zenodo.3485851

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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

@ixjlyons & @lmcinnes, 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 @leouieda know.

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

Review checklist for @ixjlyons

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @lmcinnes

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

leouieda commented 5 years ago

Hi @labarba, I had a final look at the paper and everything seems good to go on my part. The author has addressed all of the major concerns of the reviewers.

@sauln I'm happy to move on with acceptance of your paper :tada: Here are the steps you need to take now:

sauln commented 5 years ago

I'll have some time finish off these last 3 things next week.

@deargle, @mlwave, and @smangham, could you please all confirm your affiliations and orcids?

deargle commented 5 years ago

I confirm my orcid and affiliation. Thanks for heading this, @sauln.

On Tue, Sep 3, 2019, 11:36 PM Nathaniel Saul notifications@github.com wrote:

I'll have some time finish off these last 3 things next week.

@deargle https://github.com/deargle, @MLWave https://github.com/MLWave, and @smangham https://github.com/smangham, could you please all confirm your affiliations and orcids?

  • Double check authors and affiliations (including ORCIDs)
  • Make a release with the latest changes from the review and post the version number here.
  • Archive the release on Zenodo/figshare and post the DOI here (make sure the title and author list matches the JOSS paper, if possible).

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1315?email_source=notifications&email_token=AAI6Y7K5GOJIJBQIWJNMMATQH5CNZA5CNFSM4G5GPWS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD52MYGQ#issuecomment-527748122, or mute the thread https://github.com/notifications/unsubscribe-auth/AAI6Y7OCRNDYKZW7O6IUZPTQH5CNZANCNFSM4G5GPWSQ .

smangham commented 5 years ago

I can confirm my name and affiliation, my ORCID is 0000-0001-7511-5652. Apologies for the delay and thanks for handling this @sauln!

leouieda commented 5 years ago

:wave: hi @sauln any progress updates on these tasks? Let me know when you're done so we can move on to publication.

deargle commented 5 years ago

Hi @leouieda, we published an updated JOSS release to zenodo, doi 10.5281/zenodo.3485851. Version number is 1.3.3 (took a few iterations to get the .zenodo.json formatting right)

Anything else you need from us?

leouieda commented 5 years ago

@whedon check references

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

OK DOIs

- 10.1038/srep01236 is OK
- 10.2312/SPBG/SPBG07/091-100 is OK
- 10.1007/978-3-540-33259-6_7 is OK
- 10.1090/S0273-0979-09-01249-X is OK

MISSING DOIs

- None

INVALID DOIs

- None
leouieda 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:

leouieda commented 5 years ago

@deargle looks good to me! I'm happy to pass this on for final acceptance into JOSS :tada:

leouieda commented 5 years ago

@whedon set 10.5281/zenodo.3485851 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3485851 is the archive.

leouieda commented 5 years ago

@whedon set 1.3.3 as version

whedon commented 5 years ago

OK. 1.3.3 is the version.

leouieda commented 5 years ago

@openjournals/joss-eics this submission is ready for acceptance and publication :confetti_ball:

sauln commented 5 years ago

Yay!! Thank you @ixjlyons and @lmcinnes for your reviews, @leouieda for your patience, @deargle for your help pushing it through the finish line!

Kevin-Mattheus-Moerman commented 5 years ago

@whedon check references

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

OK DOIs

- 10.1038/srep01236 is OK
- 10.2312/SPBG/SPBG07/091-100 is OK
- 10.1007/978-3-540-33259-6_7 is OK
- 10.1090/S0273-0979-09-01249-X is OK

MISSING DOIs

- None

INVALID DOIs

- None
Kevin-Mattheus-Moerman commented 5 years ago

@sauln here are some minor points in relation to your paper.

Kevin-Mattheus-Moerman commented 5 years ago

@labarba can you help check the citation syntax for this paper? Are we happy about the use of & and et al. here?

labarba commented 5 years ago

In-text citations are not properly used.

When the citation is part of the sentence, it renders: Author (year). If the citation is not part of the sentence, then it should appear in parenthesis. E.g. “We take inspiration from Smith et al. (2006) to blah “ and “The code implements Theory 1 (Jones, 2012) and Theory 2 (Roberts, 2014) to obtain blah “ For the syntax to obtain brackets in the right places, see https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citation_syntax

deargle commented 5 years ago

@whedon check references

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

OK DOIs

- 10.1038/srep01236 is OK
- 10.2312/SPBG/SPBG07/091-100 is OK
- 10.1007/978-3-540-33259-6_7 is OK
- 10.1090/S0273-0979-09-01249-X is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
deargle 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:

deargle 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:

deargle 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:

deargle commented 5 years ago

@Kevin-Mattheus-Moerman I think I got everything from https://github.com/openjournals/joss-reviews/issues/1315#issuecomment-542142232. For point two, I changed the hyphenation to "Scikit-Learn-API-compatible ..."

@labarba I fixed the citation formatting.

Things look good to y'all?

Kevin-Mattheus-Moerman commented 5 years ago

@whedon accept

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

OK DOIs

- 10.1038/srep01236 is OK
- 10.2312/SPBG/SPBG07/091-100 is OK
- 10.1007/978-3-540-33259-6_7 is OK
- 10.1090/S0273-0979-09-01249-X is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1027

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1027, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
deargle commented 5 years ago

Would you want me to make a new release with those bibliography fixes?

Kevin-Mattheus-Moerman commented 5 years ago

No that is okay. The main purpose is to archive the software. The paper can have minor changes.

Kevin-Mattheus-Moerman 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

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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/1028
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01315
  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...

Kevin-Mattheus-Moerman commented 5 years ago

Congratulations @sauln! :tada: Thanks @ixjlyons, @lmcinnes for reviewing this work!!! :clap: Also thank you @leouieda for editing this submission.

whedon commented 5 years ago

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

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